Author
Arnfinn Hykkerud Steindal
Other affiliations: Rikshospitalet–Radiumhospitalet, Oslo University Hospital
Bio: Arnfinn Hykkerud Steindal is an academic researcher from University of Tromsø. The author has contributed to research in topics: QM/MM & Polarizable continuum model. The author has an hindex of 18, co-authored 24 publications receiving 1860 citations. Previous affiliations of Arnfinn Hykkerud Steindal include Rikshospitalet–Radiumhospitalet & Oslo University Hospital.
Papers
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Vilnius University1, University of Ferrara2, Aarhus University3, University of Oslo4, Royal Institute of Technology5, Electromagnetic Geoservices6, University of Trieste7, Norwegian Computing Center8, University of Southern Denmark9, University of Santiago de Compostela10, Danske Bank11, Ruhr University Bochum12, Norwegian Meteorological Institute13, Norwegian Defence Research Establishment14, University of Auckland15, Norwegian University of Science and Technology16, Information Technology University17, Technical University of Ostrava18, Linköping University19, Karlsruhe Institute of Technology20, ETH Zurich21, Australian National University22, University of Modena and Reggio Emilia23, Cisco Systems, Inc.24, University of Buenos Aires25, University of Copenhagen26, University of Erlangen-Nuremberg27, Kazimierz Wielki University in Bydgoszcz28, National Scientific and Technical Research Council29, University of Valencia30, Paul Sabatier University31, University of Melbourne32, University of Nottingham33, University of Bristol34, CLC bio35, Princeton University36, La Trobe University37, Clemson University38
TL;DR: Dalton is a powerful general‐purpose program system for the study of molecular electronic structure at the Hartree–Fock, Kohn–Sham, multiconfigurational self‐consistent‐field, Møller–Plesset, configuration‐interaction, and coupled‐cluster levels of theory.
Abstract: Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, confi ...
1,212 citations
TL;DR: The QM/MM/PCM interface is found to exhibit a faster convergence with respect to the system size as compared to the use of QM only, and the model is general, but is here implemented for the case of density functional theory.
Abstract: We present the theory and an implementation of the combined quantum mechanics/molecular mechanics/polarizable dielectric continuum (QM/MM/PCM) method. This is a fully polarizable layered model designed for effective inclusion of a medium in a quantum-mechanical calculation. The short-range part of the solvent electrostatic potential is described by an atomistic model while the long-range part of this potential is described by a dielectric continuum. The QM/MM/PCM method has been implemented in combination with QM linear response techniques allowing for the assessment of, e.g., vertical electronic excitation energies and linear dipole−dipole polarizabilities, in all cases using a nonequilibrium formulation of the environmental response. The model is general, but is here implemented for the case of density functional theory. Numerical examples are given for solvatochromic shifts relating to a set of organic molecules in aqueous solution. We find in general the QM/MM/PCM interface to exhibit a faster converg...
117 citations
TL;DR: The importance of treating the protein environment explicitly with a polarizable force field and higher-order multipoles is demonstrated, as well as the importance of including water molecules close to the chromophore in the protein barrel.
Abstract: We present for the first time a QM/MM study of the one- and two-photon absorption spectra of the GFP chromophore embedded in the full protein environment described by an advanced quantum mechanically derived polarizable force field The calculations are performed on a crystal structure of the green fluorescent protein (GFP) using the polarizable embedding density functional theory (PE-DFT) scheme The importance of treating the protein environment explicitly with a polarizable force field and higher-order multipoles is demonstrated, as well as the importance of including water molecules close to the chromophore in the protein barrel For the most advanced description we achieve good agreement with experimental findings, with a peak at 405 nm for the neutral and a peak at 475 nm for the anionic form of the GFP chromophore The presence of a dark OPA state, as suggested by other studies to explain the discrepancies between OPA and TPA spectra, is not supported by our calculations
73 citations
TL;DR: It is found that steric factors and chromophore-protein interactions act in concert to enhance the 2PA activity inside the protein while adversely blue-shifting the 1PA maximum.
Abstract: We present a detailed study of the protein environmental effects on the one- and two-photon absorption (1PA and 2PA, respectively) properties of the S0-S1 transition in the DsRed protein using the polarizable embedding density functional theory formalism. We find that steric factors and chromophore-protein interactions act in concert to enhance the 2PA activity inside the protein while adversely blue-shifting the 1PA maximum. A two-state model reveals that the 2PA intensity gain is primarily governed by the increased change in the permanent dipole moment between the ground and the excited states acquired inside the protein. Our results indicate that this mainly is attributable to counter-directional contributions stemming from Lys163 and the conserved Arg95 with the former additionally identified as a key residue in the color tuning mechanism. The results provide new insight into the tuning mechanism of DsRed and suggest a possible strategy for simultaneous improvement of its 1PA and 2PA properties.
54 citations
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01 Feb 1995
TL;DR: In this paper, the unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio using DFT, MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set.
Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg
1,652 citations
Vilnius University1, University of Ferrara2, Aarhus University3, University of Oslo4, Royal Institute of Technology5, Electromagnetic Geoservices6, University of Trieste7, Norwegian Computing Center8, University of Southern Denmark9, University of Santiago de Compostela10, Danske Bank11, Ruhr University Bochum12, Norwegian Meteorological Institute13, Norwegian Defence Research Establishment14, University of Auckland15, Norwegian University of Science and Technology16, Information Technology University17, Technical University of Ostrava18, Linköping University19, Karlsruhe Institute of Technology20, ETH Zurich21, Australian National University22, University of Modena and Reggio Emilia23, Cisco Systems, Inc.24, University of Buenos Aires25, University of Copenhagen26, University of Erlangen-Nuremberg27, Kazimierz Wielki University in Bydgoszcz28, National Scientific and Technical Research Council29, University of Valencia30, Paul Sabatier University31, University of Melbourne32, University of Nottingham33, University of Bristol34, CLC bio35, Princeton University36, La Trobe University37, Clemson University38
TL;DR: Dalton is a powerful general‐purpose program system for the study of molecular electronic structure at the Hartree–Fock, Kohn–Sham, multiconfigurational self‐consistent‐field, Møller–Plesset, configuration‐interaction, and coupled‐cluster levels of theory.
Abstract: Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, confi ...
1,212 citations
TL;DR: Near-infrared-emissive polymer-carbon nanodots possess two-photon fluorescence; in vivo bioimaging and red-light-emitting diodes based on these PCNDs are demonstrated.
Abstract: Near-infrared-emissive polymer-carbon nanodots (PCNDs) are fabricated by a newly developed facile, high-output strategy. The PCNDs emit at a wavelength of 710 nm with a quantum yield of 26.28%, which is promising for deep biological imaging and luminescent devices. Moreover, the PCNDs possess two-photon fluorescence; in vivo bioimaging and red-light-emitting diodes based on these PCNDs are demonstrated.
620 citations
Uppsala University1, Max Planck Society2, University of Ferrara3, University of Geneva4, State University of New York System5, University of Minnesota6, University of Rostock7, Katholieke Universiteit Leuven8, Lund University9, Stockholm University10, Harvard University11, Interdisciplinary Center for Scientific Computing12, ETH Zurich13, University of Alcalá14, University of Valencia15, University College London16, University of Vienna17, Imperial College London18, Heidelberg University19, Massey University20, University of Strasbourg21, University of Siena22, Bowling Green State University23, Loughborough University24, Hebrew University of Jerusalem25, National University of Singapore26
TL;DR: The OpenMolcas environment is described and features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism and properties are described.
Abstract: In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.
559 citations
TL;DR: The populations exhibiting maximally depigmented skin are those inhabiting environments with the lowest annual and summer peak levels of UVB, generally low and peak only once during the year.
Abstract: Human skin pigmentation is the product of two clines produced by natural selection to adjust levels of constitutive pigmentation to levels of UV radiation (UVR). One cline was generated by high UVR near the equator and led to the evolution of dark, photoprotective, eumelanin-rich pigmentation. The other was produced by the requirement for UVB photons to sustain cutaneous photosynthesis of vitamin D3 in low-UVB environments, and resulted in the evolution of depigmented skin. As hominins dispersed outside of the tropics, they experienced different intensities and seasonal mixtures of UVA and UVB. Extreme UVA throughout the year and two equinoctial peaks of UVB prevail within the tropics. Under these conditions, the primary selective pressure was to protect folate by maintaining dark pigmentation. Photolysis of folate and its main serum form of 5-methylhydrofolate is caused by UVR and by reactive oxygen species generated by UVA. Competition for folate between the needs for cell division, DNA repair, and melanogenesis is severe under stressful, high-UVR conditions and is exacerbated by dietary insufficiency. Outside of tropical latitudes, UVB levels are generally low and peak only once during the year. The populations exhibiting maximally depigmented skin are those inhabiting environments with the lowest annual and summer peak levels of UVB. Development of facultative pigmentation (tanning) was important to populations settling between roughly 23° and 46° , where levels of UVB varied strongly according to season. Depigmented and tannable skin evolved numerous times in hominin evolution via independent genetic pathways under positive selection.
556 citations