Article
Biochemistry & Molecular Biology
Miquel Huix-Rotllant
Summary: The study investigates the electrostatic effects of methanol and water on thymine's excited states, revealing that solvent molecules define the branching plane of the S0/S1 intersection. The electrostatic embedding TD-DFT/MM method allows for a fast exploration of potential energy surfaces and a qualitative understanding of thymine's photophysics in solvent droplets, despite the incorrect topology of the ground/excited state intersections.
Article
Physics, Multidisciplinary
Orest Hryhorchak, Andrij Rovenchak
Summary: We have analyzed the higher multipole moments in the expansion of the electrostatic potential generated by various distributions of charges over Platonic solids. The lowest non-zero multipole moment for the tetrahedron is the octupole, while for the octahedron and cube it is the hexadecapole. For the icosahedron and dodecahedron, non-zero elements appear first in the 2(6)-pole moment tensors.
Article
Astronomy & Astrophysics
Goncalo Castro, Leonardo Gualtieri, Paolo Pani
Summary: Numerical evidence suggests a surprising hidden symmetry among the rotational tidal Love numbers with opposite parities, which are associated with perturbations belonging to separate sectors. This symmetry, proposed based on a Lagrangian description of the tidal interaction in a binary system, holds independently of the equation of state of the star.
Article
Astronomy & Astrophysics
Ulf Danielsson, Suvendu Giri
Summary: In this paper, a string theory inspired alternative to gravitational collapse is proposed, and the rotating black shells are examined for stability, with flux parameters determined by constraints from dynamical analysis. The preferred quadrupole moment is found to be 7% less than Kerr, based on physical assumptions.
Article
Astronomy & Astrophysics
Samuel D. Upton, Adam Pound
Summary: Research shows that highly regular gauges can more efficiently extract system parameters from EMRI waveforms in numerical calculations. By deriving expressions for the metric perturbation and the distributional source of the second-order field, it is possible to calculate the second-order self-force more accurately.
Article
Astronomy & Astrophysics
Nicholas Loutrel, Paolo Pani, Nicolas Yunes
Summary: In general relativity, the no-hair theorems determine the multipolar structure of isolated black holes, but in modified gravity or when dealing with non-black hole compact objects, the multipolar structure of the exterior spacetime may differ. The multipolar structure plays a crucial role in the dynamics and gravitational wave emissions of binary black holes, and characterizing these effects can provide valuable insights into fundamental physics. This study proposes an extension of the parametrized post-Einsteinian framework to incorporate precession effects, which can serve as a basis for future tests of general relativity using gravitational waves from precessing binaries.
Article
Chemistry, Physical
Peter Reinholdt, Jacob Kongsted, Filippo Lipparini
Summary: The article explores three strategies to approximate the QM/MM coupling based on multipole expansion techniques, benchmarking the implementations for accuracy and computational efficiency in calculating spectroscopic properties. The proposed strategies provide significant computational savings without compromising the accuracy of the calculated spectroscopic properties.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Junbo Chen, Jason B. Harper, Junming Ho
Summary: This paper introduces an economical approach to improve the accuracy and convergence of quantum mechanics/ molecular mechanics models. By using quantum-level charges on molecular mechanics atoms, the accuracy and convergence of QM/MM models can be significantly improved.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Xianwei Wang, Xilong Li, Xiao He, John Z. H. Zhang
Summary: The FMIC model accurately predicts intermolecular electrostatic interactions with significantly lower error compared to the ESP charge model. Transferability of the FMIC method was demonstrated in different molecular systems. This approach provides an efficient tool for future development of molecular force fields.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Medicinal
Bharath Raghavan, Florian K. Schackert, Andrea Levy, Sophia K. Johnson, Emiliano Ippoliti, Davide Mandelli, Jogvan Magnus Haugaard Olsen, Ursula Rothlisberger, Paolo Carloni
Summary: MiMiC is a flexible and scalable multiscale modeling framework that combines quantum mechanics (QM) and molecular mechanics (MM) codes. The paragraph introduces MiMiCPy, a user-friendly tool written in Python 3 that automates the preparation of MiMiC input files. It also highlights the modular structure of MiMiCPy, allowing for easy extensions to new program formats.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Martin J. Field
Summary: This paper explores the effectiveness of extending the technique of density fitting to treat interactions with external electrostatic potentials. The study finds that fitted densities can accurately reproduce the energies, forces, and properties obtained using unfitted densities, as long as a suitable operator is employed for the fitting. The precision is expected to improve with the development of basis sets specifically designed for these types of interactions, and the approximation could lead to substantial speed-ups in large hybrid potential simulations.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Biochemistry & Molecular Biology
Kevin Clark, Natalia B. Pigni, Kithmini Wijesiri, Jose A. Gascon
Summary: Increased interest in sequencing cyanobacterial genomes has led to the discovery of new homologs to both the N-terminal and C-terminal domains of the Orange Carotenoid Protein (OCP). One of these homologs (HCP2) exclusively binds canthaxanthin and shows a significantly red-shifted absorption spectrum.
Article
Chemistry, Multidisciplinary
Niklas Niemeyer, Patrick Eschenbach, Moritz Bensberg, Johannes Toelle, Lars Hellmann, Lukas Lampe, Anja Massolle, Anton Rikus, David Schnieders, Jan P. Unsleber, Johannes Neugebauer
Summary: SERENITY is an open-source quantum chemistry software that focuses on quantum-mechanical multilevel and embedding approaches. This study provides an overview of the developments in SERENITY since its original publication in 2018, including efficient electronic-structure methods for ground and excited states. SERENITY's modular structure allows for combination with density-functional theory-based embedding through various practical realizations and variants of subsystem DFT.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Astronomy & Astrophysics
H. Garcia-Compean, V. S. Manko, C. J. Ramirez-Valdez
Summary: This paper extends our previous research results to the case of axially symmetric dyonic black holes and introduces the classical Ernst formalism with the magnetic potential 0m. We analyze in detail the case of the dyonic Kerr-Newman black hole and correctly evaluate the Komar mass, proving the validity of the standard Tomimatsu mass formula.
Article
Astronomy & Astrophysics
V. S. Manko, E. Ruiz
Summary: In this paper, two physically meaningful configurations of a pair of equal Kerr-Newman corotating black holes separated by a massless strut are elaborated using the general equatorially symmetric two-soliton solution. The thermodynamic properties of these binary configurations are studied and the first law of thermodynamics taking correctly into account the magnetic field contribution is formulated for each case.
Article
Chemistry, Physical
Till Kirsch, Jogvan Magnus Haugaard Olsen, Viacheslav Bolnykh, Simone Meloni, Emiliano Ippoliti, Ursula Rothlisberger, Michele Cascella, Juergen Gauss
Summary: This study presents an interface of the wavefunction-based quantum chemical software CFOUR to the multiscale modeling framework MiMiC and validates its robustness and performance, including fast convergence and optimal energy conservation. The compatibility with the use of a QM/QM multiple time-step algorithm for reducing the cost of simulations using higher level wavefunction-based approaches is also pointed out.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Jonathan R. Church, Gil S. Amoyal, Veniamin A. Borin, Suliman Adam, Jogvan Magnus Haugaard Olsen, Igor Schapiro
Summary: Proteorhodopsin (PR) is a photoactive proton pump found in marine bacteria. By substituting glutamine with leucine, the absorption wavelength of PR can be tuned, allowing it to adapt to different depths in the ocean. Our study reveals the tuning mechanism and provides guidance for rational design of spectral shifts.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Vildan A. Turkmen, Jordi C. J. Hintzen, Anthony Tumber, Laust Moesgaard, Eidarus Salah, Jacob Kongsted, Christopher J. Schofield, Jasmin Mecinovic
Summary: Non-haem Fe(ii) and 2-oxoglutarate (2OG) dependent oxygenases catalyze oxidation of proteins, and this study focuses on the substrate selectivity and inhibition of human ribosomal oxygenases (ROX) MINA53 and NO66. The results show that MINA53 and NO66 have narrow substrate selectivity compared to other human JmjC hydroxylases. Inhibition assays also suggest that the activities of MINA53/NO66 might be regulated in vivo by competition with non-oxidized proteins/peptides.
RSC CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Organic
Mads W. Mulberg, Mick Hornum, Peter Reinholdt, Brian Bjarke Jensen, Maria Szomek, Jonathan R. Brewer, Daniel Wuestner, Jacob Kongsted, Poul Nielsen
Summary: Fine-tuning of fluorophores is crucial for the development of next generation fluorescent dyes for microscopy. We report a robust and concise method for synthesizing 14 new Nile Red analogues with extended pi ring systems and diverse functionalities. These new fluorophores showed favorable two-photon excitation efficiency and general fluorescent properties. One derivative exhibited extreme solvent sensitivity and another showed significantly redshifted emission, large Stokes shift, and high two-photon brightness.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Nurguel Bilgin, Laust Moesgaard, Mohammad M. Rahman, Vildan A. Tuerkmen, Jacob Kongsted, Jasmin Mecinovic
Summary: In this study, we investigated the molecular recognition of histone H3 peptides with methacryllysine and crotonyllysine by the AF9 YEATS domain. Our findings suggest that AF9 YEATS has a higher binding affinity for crotonyllysine than methacryllysine, indicating its ability to distinguish between the two regioisomers. Molecular dynamics simulations revealed that the desolvation of the AF9 YEATS domain by crotonyllysine/methacryllysine contributes to the recognition of both epigenetic marks. These findings are important for the development of AF9 YEATS inhibitors, a promising area of biomedical research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Peter Reinholdt, Willem Van den Heuvel, Jacob Kongsted
Summary: The polarizable density embedding (PDE) model is an advanced fragment-based QM/QM embedding model that improves the description of electrostatics and includes non-electrostatic repulsion. We developed analytic geometric gradients for the PDE model to optimize the geometry of QM regions within large molecular environments. We also propose a hybrid PDE-LJ model that produces good quality solute-solvent structures for density functional theory (DFT) calculations.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)
Article
Chemistry, Medicinal
Bharath Raghavan, Florian K. Schackert, Andrea Levy, Sophia K. Johnson, Emiliano Ippoliti, Davide Mandelli, Jogvan Magnus Haugaard Olsen, Ursula Rothlisberger, Paolo Carloni
Summary: MiMiC is a flexible and scalable multiscale modeling framework that combines quantum mechanics (QM) and molecular mechanics (MM) codes. The paragraph introduces MiMiCPy, a user-friendly tool written in Python 3 that automates the preparation of MiMiC input files. It also highlights the modular structure of MiMiCPy, allowing for easy extensions to new program formats.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Willem Van den Heuvel, Peter Reinholdt, Jacob Kongsted
Summary: The PDE model is expanded to include exchange and nonadditive exchange-correlation effects, resulting in the PDE-X model. The PDE-X model accurately captures the range dependence of solvent interaction and improves the accuracy of excitation energies for organic chromophores. The improved embedding description leads to systematic solvent effects that do not average out when applying configurational sampling.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemistry & Molecular Biology
Mays S. Q. Al-Fakhar, Nurgul Bilgin, Laust Moesgaard, Apolonia Witecka, Jakub Drozak, Jacob Kongsted, Jasmin Mecinovic
Summary: This study reveals that the amino acid Trp79 in beta-actin plays an important role in the catalytic activity of SETD3, and maintaining a bulky and hydrophobic amino acid at position 79 is crucial for efficient methylation of His73 by SETD3. The findings highlight the significance of the distant Trp79 binding site in efficient SETD3 catalysis, which contributes to the identification of new SETD3 substrates and the development of chemical probes targeting SETD3, an important biomolecule in biomedicine.
Article
Chemistry, Physical
David Carrasco-Busturia, Joigvan Magnus Haugaard Olsen
Summary: Polarizable embedding is a classical embedding method that allows mutual polarization between quantum and classical regions. The quality of the embedding potential is crucial for accurate results, and can be obtained by dividing the classical region into smaller fragments and deriving parameters from ab initio calculations. This study assesses the effects of hydrogen-bond fragmentation in the MFCC procedure for deriving embedding-potential parameters.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Sonata Kvedaraviciute, David Carrasco-Busturia, Klaus B. Moller, Joigvan Magnus Haugaard Olsen
Summary: We propose a fully self-consistent polarizable embedding (PE) model that avoids unphysical boundary polarization by using the minimum-image convention (MIC) in induced electrostatics. This method provides a more physically accurate description of polarization throughout the molecular system. By comparing induced dipoles, electrostatic potentials, and optical properties of solute-solvent and biomolecular systems, we show that commonly used cutoff models, like the droplet model, have limitations in PE calculations due to unphysical polarization at the outer boundary.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biophysics
Jonathan R. Church, Jogvan Magnus Haugaard Olsen, Igor Schapiro
Summary: Multiscale simulations have been used to calculate excitation energies in complex systems, with the chromophore treated quantum mechanically and the protein and environment described classically. Electrostatic embedding and polarizable embedding were compared for their effect on excitation energies in two different proteins. Results showed that polarizable embedding produces absorption maxima closer to experimental values and recovers a significant portion of the quantum mechanical improvement in excitation energies. A detailed analysis revealed that aromatic residues have the largest influence on excitation energy.
BIOPHYSICS AND PHYSICOBIOLOGY
(2023)
Article
Chemistry, Physical
Willem Van den Heuvel, Peter Reinholdt, Jacob Kongsted
Summary: The polarizable density embedding (PDE) model is extended to include exchange and nonadditive exchange-correlation in the embedding potential, resulting in the PDE-X model. This model accurately captures the range dependence of solvent interaction and significantly improves the accuracy of excitation energies for organic chromophores. The improved embedding description leads to systematic solvent effects that persist under configurational sampling.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Hongbo Wu, Zaifei Ma, Mengyang Li, Hao Lu, Ailing Tang, Erjun Zhou, Jin Wen, Yanming Sun, Wolfgang Tress, Jogvan Magnus Haugaard Olsen, Simone Meloni, Zhishan Bo, Zheng Tang
Summary: Donor halogenation improves the performance of organic solar cells by increasing the energy of the charge transfer state and reducing reorganization energy. The impact of donor halogenation varies depending on the acceptor type, with stronger effects observed for Y-series acceptors. Halogen substitution on side groups of the donor molecule is more effective in reducing voltage losses.
ENERGY & ENVIRONMENTAL SCIENCE
(2023)
Article
Chemistry, Physical
Andrew M. Teale, Trygve Helgaker, Andreas Savin, Carlo Adamo, Balint Aradi, Alexei Arbuznikov, Paul W. Ayers, Evert Jan Baerends, Vincenzo Barone, Patrizia Calaminici, Eric Cances, Emily A. Carter, Pratim Kumar Chattaraj, Henry Chermette, Ilaria Ciofini, T. Daniel Crawford, Frank De Proft, John F. Dobson, Claudia Draxl, Thomas Frauenheim, Emmanuel Fromager, Patricio Fuentealba, Laura Gagliardi, Giulia Galli, Jiali Gao, Paul Geerlings, Nikitas Gidopoulos, Peter M. W. Gill, Paola Gori-Giorgi, Andreas Gorling, Tim Gould, Stefan Grimme, Oleg Gritsenko, Hans Jorgen Aagaard Jensen, Erin R. Johnson, Robert O. Jones, Martin Kaupp, Andreas M. Koster, Leeor Kronik, Anna Krylov, Simen Kvaal, Andre Laestadius, Mel Levy, Mathieu Lewin, Shubin Liu, Pierre-Francois Loos, Neepa T. Maitra, Frank Neese, John P. Perdew, Katarzyna Pernal, Pascal Pernot, Piotr Piecuch, Elisa Rebolini, Lucia Reining, Pina Romaniello, Adrienn Ruzsinszky, Dennis R. Salahub, Matthias Scheffler, Peter Schwerdtfeger, Viktor N. Staroverov, Jianwei Sun, Erik Tellgren, David J. Tozer, Samuel B. Trickey, Carsten A. Ullrich, Alberto Vela, Giovanni Vignale, Tomasz A. Wesolowski, Xin Xu, Weitao Yang
Summary: This paper provides an informal review and discussion on the history, present status, and future of density-functional theory (DFT) by 70 workers in the field. The format of a roundtable discussion allowed participants to express their views through 302 individual contributions to a preset list of 26 questions. Supported by a bibliography of 777 entries, the paper offers a comprehensive snapshot of DFT in 2022.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Michal Novotny, Matus Dubecky, Frantisek Karlicky
Summary: This paper investigates the accuracy of different DFT-based computational approaches in calculating the equilibrium lattice constants and exfoliation energy of hexagonal boron nitride (h-BN). The results are compared with experiments and reference QMC calculations to evaluate the accuracy of these computational methods.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Luigi Crisci, Federico Coppola, Alessio Petrone, Nadia Rega
Summary: The charge transfer dynamics in asymmetrically substituted indenotetracene molecules upon photo-excitation were investigated using real-time time-dependent density functional theory simulations. The study found that the electron-donating character of the substituents affects the overall electronic energy spacing and ultrafast charge transfer dynamics.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Vasilii Korotenko, Hendrik Zipse
Summary: The stability of various radicals and molecules has been studied using different theoretical methods, and good correlations between theoretical calculations and experimental results have been found. The effects of hydrogen bonding interactions on the stability of oxygen-centered radicals have also been investigated.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Oleg Egorov, Michael Rey, Dominika Viglaska, Andrei V. Nikitin
Summary: In this work, the rovibrational energy levels of four isotopologues of methylene were calculated using a new accurate ab initio potential energy surface. The accuracy of the calculations was improved by considering scalar relativistic effects, DBOC, and high-order electronic correlations. For the first time, all available experimental rovibrational transitions were reproduced with high accuracy, without any empirical corrections.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)