Arnout Ceulemans - Academia.edu (original) (raw)
Papers by Arnout Ceulemans
Cornell University - arXiv, Sep 20, 2017
A set formed by five reversibly-switchable fluorescent proteins (RSFPs) display spread over 40 nm... more A set formed by five reversibly-switchable fluorescent proteins (RSFPs) display spread over 40 nm in absorption maxima and only 18 nm in emission. The five proteins-Dronpa, rsFastLime, rsKame, Padron(anionic form) and bsDronpa-carry exactly the same chromophore and differ just in a few mutations. Thus they form an ideal set for mechanistic investigation. Starting with the results of molecular dynamics simulations we use QM/MM calculations to investigate the effects controlling the spectral tuning. In this contribution we show that the models, which are based on CASPT2//CASSCF level of QM theory, reproduce the observed absorption trend with only a limited blue-shift of 4.5 kcal/mol and emission trend with even smaller blue-shift of 1.5 kcal/mol. Using CASSCF QM/MM calculations we analyze the chromophore's charge-transfer patterns during the absorption and emission, which, in turn trigger a cascade of hydrogen-bond-network rearrangements indicating a preparation to an isomerization event. We also show how the contribution of individual aminoacids to the chromophore conformational changes correlates with spectral tuning of the absorption and emission. Furthermore, we identify how the conical intersection topography correlates with protein's photophysical properties. In conclusion, we establish a detailed mechanistic explanation of variations in photo-switching speed as well as higher sensitivity of RSFPs to mutation observed for light absorption relative to light emission.
Mendeleev to Oganesson
In 1969, the centennial of Mendeleev’s discovery of the periodic table was commemorated by an int... more In 1969, the centennial of Mendeleev’s discovery of the periodic table was commemorated by an international conference devoted to the periodicity and symmetry of the elementary structure of matter. The conference was held in the Vatican and brought together a selected audience of first-rate atomic and nuclear scientists. In 1971, the proceedings were published in a joint publication [1] of the Academy of Sciences of Torino and the National Academy in Rome. Among the many interesting contributions, the American cosmologist John Archibald Wheeler described a mind-boggling journey from “Mendeleev’s atom to the collapsing star.” According to Wheeler [2], Mendeleev was convinced that the atom is not “deathlike inactivity” but a dynamic reality and Mendeleev expressed his hope that the discovery of an orderly pattern would “hasten the advent of a true chemical mechanics.” This hope has certainly been met by Schrödinger’s wave mechanics, which provides an accurate tool to simulate the prop...
The Journal of Chemical Physics, 2020
A threefold degenerate electronic state is Jahn-Teller unstable with respect to symmetry lowering... more A threefold degenerate electronic state is Jahn-Teller unstable with respect to symmetry lowering distortions, which transform as the five quadrupolar modes. The solution of the corresponding vibronic Hamiltonian is constructed using the analytical method introduced by Bargmann, as an alternative to existing group-theoretical methods based on coefficients of fractional parentage. It involves the construction of an Ansatz which incorporates SO(5) to SO(3) symmetry breaking. The resulting Jahn-Teller equations are derived, and solved in terms of radial polynomials and Gegenbauer functions.
Advances in Quantum Chemistry, 2003
ABSTRACT
Cornell University - arXiv, Sep 20, 2017
A set formed by five reversibly-switchable fluorescent proteins (RSFPs) display spread over 40 nm... more A set formed by five reversibly-switchable fluorescent proteins (RSFPs) display spread over 40 nm in absorption maxima and only 18 nm in emission. The five proteins-Dronpa, rsFastLime, rsKame, Padron(anionic form) and bsDronpa-carry exactly the same chromophore and differ just in a few mutations. Thus they form an ideal set for mechanistic investigation. Starting with the results of molecular dynamics simulations we use QM/MM calculations to investigate the effects controlling the spectral tuning. In this contribution we show that the models, which are based on CASPT2//CASSCF level of QM theory, reproduce the observed absorption trend with only a limited blue-shift of 4.5 kcal/mol and emission trend with even smaller blue-shift of 1.5 kcal/mol. Using CASSCF QM/MM calculations we analyze the chromophore's charge-transfer patterns during the absorption and emission, which, in turn trigger a cascade of hydrogen-bond-network rearrangements indicating a preparation to an isomerization event. We also show how the contribution of individual aminoacids to the chromophore conformational changes correlates with spectral tuning of the absorption and emission. Furthermore, we identify how the conical intersection topography correlates with protein's photophysical properties. In conclusion, we establish a detailed mechanistic explanation of variations in photo-switching speed as well as higher sensitivity of RSFPs to mutation observed for light absorption relative to light emission.
International Journal of Quantum Chemistry, 2018
A well defined class of planar or quasi-planar elongated boron clusters, of type B q− 7+3n , serv... more A well defined class of planar or quasi-planar elongated boron clusters, of type B q− 7+3n , serves as a basis to identify the valence bond picture of delocalized boron networks. The origin of the series is the B − 7 cluster, which exhibits σ-aromaticity. The cluster generating step is the repetitive expansion by three boron atoms in the direction of elongation. Specific electron counting rules are obtained for π-bonding, peripheral σ-bonding and multi-center inner σ-bonding. A valence bond structure is introduced which explains the remarkable regularity in the bonding pattern. The analysis supports 4c-2e bonds as an alternative to the common 3c-2e bonds. The results are validated by symmetry induction and ab initio calculations.
The Theory of the Jahn-Teller Effect
Physical Chemistry Chemical Physics, 2018
Valence bonds within the perimeter of disk-like boron clusters with a concentric topology follow ... more Valence bonds within the perimeter of disk-like boron clusters with a concentric topology follow simple 4n and 8n electron counting rules.
The Journal of Chemical Physics, 2020
A threefold degenerate electronic state is Jahn-Teller unstable with respect to symmetry lowering... more A threefold degenerate electronic state is Jahn-Teller unstable with respect to symmetry lowering distortions, which transform as the five quadrupolar modes. The solution of the corresponding vibronic Hamiltonian is constructed using the analytical method introduced by Bargmann, as an alternative to existing group-theoretical methods based on coefficients of fractional parentage. It involves the construction of an Ansatz which incorporates SO(5) to SO(3) symmetry breaking. The resulting Jahn-Teller equations are derived, and solved in terms of radial polynomials and Gegenbauer functions.
Journal of the Chemical Society, Faraday Transactions, 1995
Euler's theorem is extended to the permutation symmetries of objects associated with vertices... more Euler's theorem is extended to the permutation symmetries of objects associated with vertices, edges and faces of general polyhedra imbedded in the sphere, torus or a surface of higher genus. An equivalent general theorem is derived for benzenoid hydrocarbons. Further relations are found for deltahedral and three-coordinate polyhedra imbedded in the various surfaces. Application of the new theorems to vibrational analysis and molecular electronic structure is sketched, with particular reference to bonding in possible toroidal analogues of the fullerenes.
Advances in Quantum Chemistry, 2003
ABSTRACT
The shell structure of matter is a unifying principle, from the fixed orbits of the planets, to t... more The shell structure of matter is a unifying principle, from the fixed orbits of the planets, to the gyrating electrons in an atom, and the dance of the quarks in protons and neutrons. It puts Mendeleev’s Periodic System, proposed 150 years ago, into the historical perspective of two other great taxonomies: the earlier planetary law of Titius-Bode, and the later quark hypothesis by Gell-Mann. In the case of the quarks, use was made of the theory of symmetry groups, which was created around 1830 in a flash of genius by Évariste Galois. Its subsequent application to the symmetry of continua is due to Sophus Lie. In this respect the classification of hadronic matter by group theory shows a more advanced and mature form of theory, as compared to the quantum mechanical treatment of the Periodic System. In 1969, at the centennial of Mendeleev’s discovery, Löwdin noted how remarkable it was that the periodicity of the table had not been derived from first principles. This challenge is calli...
Physical Review B, 1999
Effects of electron correlation, intrasite vibronic interaction, and merohedral disorder on the e... more Effects of electron correlation, intrasite vibronic interaction, and merohedral disorder on the electronic structure of K 4 C 60 are investigated with a model approach taking into account all essential interactions in the lowest unoccupied molecular orbital ͑LUMO͒ band. The self-energy was calculated within the GW approximation with self-consistency after the quasiparticle Green function starting from Hartree-Fock band structure. The insulating state arises due to interorbital charge disproportionation within the LUMO band while the band gap is strongly reduced by effects of long-range electron correlation. The results of the calculations are in reasonable agreement with experiment, providing evidence for a Jahn-Teller induced transition from a Mott-Hubbard to a band insulator state. ͓S0163-1829͑99͒51020-5͔
International Journal of Quantum Chemistry, 2018
A well defined class of planar or quasi-planar elongated boron clusters, of type B q− 7+3n , serv... more A well defined class of planar or quasi-planar elongated boron clusters, of type B q− 7+3n , serves as a basis to identify the valence bond picture of delocalized boron networks. The origin of the series is the B − 7 cluster, which exhibits σ-aromaticity. The cluster generating step is the repetitive expansion by three boron atoms in the direction of elongation. Specific electron counting rules are obtained for π-bonding, peripheral σ-bonding and multi-center inner σ-bonding. A valence bond structure is introduced which explains the remarkable regularity in the bonding pattern. The analysis supports 4c-2e bonds as an alternative to the common 3c-2e bonds. The results are validated by symmetry induction and ab initio calculations.
Physical Review B, 1996
The instability of a high-symmetry distribution of conduction electrons in t-type orbitals in cub... more The instability of a high-symmetry distribution of conduction electrons in t-type orbitals in cubic lattices is investigated within the mean-field approach. All essential bielectronic and one-site vibronic interactions involving the threefold degenerate orbitals are taken into account. It is shown that the degeneracy of the site orbitals may give rise to a special kind of electronic instability, described as orbital disproportionation of the conduction-electron density at each site. The criterion for instability of the cubic band structure with respect to a homogeneous disproportionation, including both spin-and charge-density redistributions, is established. Low-symmetry nuclear distortions may reinforce the tendency for disproportionation of charge density between t orbitals. A model calculation suggests that electronic charge disproportionation may be responsible for the unusual band structure of alkali-metal-doped fullerides. ͓S0163-1829͑96͒05423-9͔
Physical Chemistry Chemical Physics, 2018
Valence bonds within the perimeter of disk-like boron clusters with a concentric topology follow ... more Valence bonds within the perimeter of disk-like boron clusters with a concentric topology follow simple 4n and 8n electron counting rules.
AIP Conference Proceedings, 2000
The electronic structure of K3C60 is investigated in a band approach allowing for arbitrary distr... more The electronic structure of K3C60 is investigated in a band approach allowing for arbitrary distribution of the charge density among the three LUMO orbitals at each fullerene site (a model analogue of the LDA+U method). The predictions for optical absorption and EELS of these broken-symmetry band structure calculations are compared with available experimental data. We find that such calculations reproduce the three absorption bands in the low energy region of the optical conductivity spectrum and give the correct dc limit for the conductivity. Simulations of the loss function show the right position and width of the metallic plasmon peak. Similar calculations within the conventional band structure approach fail to reproduce the above spectroscopic features.
Journal of the Chemical Society, Faraday Transactions, 1995
Euler's theorem is extended to the permutation symmetries of objects associated with vertices... more Euler's theorem is extended to the permutation symmetries of objects associated with vertices, edges and faces of general polyhedra imbedded in the sphere, torus or a surface of higher genus. An equivalent general theorem is derived for benzenoid hydrocarbons. Further relations are found for deltahedral and three-coordinate polyhedra imbedded in the various surfaces. Application of the new theorems to vibrational analysis and molecular electronic structure is sketched, with particular reference to bonding in possible toroidal analogues of the fullerenes.
Journal of Physics A: Mathematical and Theoretical, 2017
The Bargmann-Fock representation of the Rabi Hamiltonian is expressed by a system of two coupled ... more The Bargmann-Fock representation of the Rabi Hamiltonian is expressed by a system of two coupled first-order differential equations in the complex field, which may be rewritten in a canonical form under the Birkhoff transformation. The transformation gives rise to leapfrog recurrence relations, from which the eigenvalues and eigenvectors could be obtained. The interesting feature of this approach is that it generates integer quantum numbers, which relate the solutions to the Juddian baselines. The relationship with Braak's integrability claim [PRL 107, 100401 (2011)] is discussed.
Cornell University - arXiv, Sep 20, 2017
A set formed by five reversibly-switchable fluorescent proteins (RSFPs) display spread over 40 nm... more A set formed by five reversibly-switchable fluorescent proteins (RSFPs) display spread over 40 nm in absorption maxima and only 18 nm in emission. The five proteins-Dronpa, rsFastLime, rsKame, Padron(anionic form) and bsDronpa-carry exactly the same chromophore and differ just in a few mutations. Thus they form an ideal set for mechanistic investigation. Starting with the results of molecular dynamics simulations we use QM/MM calculations to investigate the effects controlling the spectral tuning. In this contribution we show that the models, which are based on CASPT2//CASSCF level of QM theory, reproduce the observed absorption trend with only a limited blue-shift of 4.5 kcal/mol and emission trend with even smaller blue-shift of 1.5 kcal/mol. Using CASSCF QM/MM calculations we analyze the chromophore's charge-transfer patterns during the absorption and emission, which, in turn trigger a cascade of hydrogen-bond-network rearrangements indicating a preparation to an isomerization event. We also show how the contribution of individual aminoacids to the chromophore conformational changes correlates with spectral tuning of the absorption and emission. Furthermore, we identify how the conical intersection topography correlates with protein's photophysical properties. In conclusion, we establish a detailed mechanistic explanation of variations in photo-switching speed as well as higher sensitivity of RSFPs to mutation observed for light absorption relative to light emission.
Mendeleev to Oganesson
In 1969, the centennial of Mendeleev’s discovery of the periodic table was commemorated by an int... more In 1969, the centennial of Mendeleev’s discovery of the periodic table was commemorated by an international conference devoted to the periodicity and symmetry of the elementary structure of matter. The conference was held in the Vatican and brought together a selected audience of first-rate atomic and nuclear scientists. In 1971, the proceedings were published in a joint publication [1] of the Academy of Sciences of Torino and the National Academy in Rome. Among the many interesting contributions, the American cosmologist John Archibald Wheeler described a mind-boggling journey from “Mendeleev’s atom to the collapsing star.” According to Wheeler [2], Mendeleev was convinced that the atom is not “deathlike inactivity” but a dynamic reality and Mendeleev expressed his hope that the discovery of an orderly pattern would “hasten the advent of a true chemical mechanics.” This hope has certainly been met by Schrödinger’s wave mechanics, which provides an accurate tool to simulate the prop...
The Journal of Chemical Physics, 2020
A threefold degenerate electronic state is Jahn-Teller unstable with respect to symmetry lowering... more A threefold degenerate electronic state is Jahn-Teller unstable with respect to symmetry lowering distortions, which transform as the five quadrupolar modes. The solution of the corresponding vibronic Hamiltonian is constructed using the analytical method introduced by Bargmann, as an alternative to existing group-theoretical methods based on coefficients of fractional parentage. It involves the construction of an Ansatz which incorporates SO(5) to SO(3) symmetry breaking. The resulting Jahn-Teller equations are derived, and solved in terms of radial polynomials and Gegenbauer functions.
Advances in Quantum Chemistry, 2003
ABSTRACT
Cornell University - arXiv, Sep 20, 2017
A set formed by five reversibly-switchable fluorescent proteins (RSFPs) display spread over 40 nm... more A set formed by five reversibly-switchable fluorescent proteins (RSFPs) display spread over 40 nm in absorption maxima and only 18 nm in emission. The five proteins-Dronpa, rsFastLime, rsKame, Padron(anionic form) and bsDronpa-carry exactly the same chromophore and differ just in a few mutations. Thus they form an ideal set for mechanistic investigation. Starting with the results of molecular dynamics simulations we use QM/MM calculations to investigate the effects controlling the spectral tuning. In this contribution we show that the models, which are based on CASPT2//CASSCF level of QM theory, reproduce the observed absorption trend with only a limited blue-shift of 4.5 kcal/mol and emission trend with even smaller blue-shift of 1.5 kcal/mol. Using CASSCF QM/MM calculations we analyze the chromophore's charge-transfer patterns during the absorption and emission, which, in turn trigger a cascade of hydrogen-bond-network rearrangements indicating a preparation to an isomerization event. We also show how the contribution of individual aminoacids to the chromophore conformational changes correlates with spectral tuning of the absorption and emission. Furthermore, we identify how the conical intersection topography correlates with protein's photophysical properties. In conclusion, we establish a detailed mechanistic explanation of variations in photo-switching speed as well as higher sensitivity of RSFPs to mutation observed for light absorption relative to light emission.
International Journal of Quantum Chemistry, 2018
A well defined class of planar or quasi-planar elongated boron clusters, of type B q− 7+3n , serv... more A well defined class of planar or quasi-planar elongated boron clusters, of type B q− 7+3n , serves as a basis to identify the valence bond picture of delocalized boron networks. The origin of the series is the B − 7 cluster, which exhibits σ-aromaticity. The cluster generating step is the repetitive expansion by three boron atoms in the direction of elongation. Specific electron counting rules are obtained for π-bonding, peripheral σ-bonding and multi-center inner σ-bonding. A valence bond structure is introduced which explains the remarkable regularity in the bonding pattern. The analysis supports 4c-2e bonds as an alternative to the common 3c-2e bonds. The results are validated by symmetry induction and ab initio calculations.
The Theory of the Jahn-Teller Effect
Physical Chemistry Chemical Physics, 2018
Valence bonds within the perimeter of disk-like boron clusters with a concentric topology follow ... more Valence bonds within the perimeter of disk-like boron clusters with a concentric topology follow simple 4n and 8n electron counting rules.
The Journal of Chemical Physics, 2020
A threefold degenerate electronic state is Jahn-Teller unstable with respect to symmetry lowering... more A threefold degenerate electronic state is Jahn-Teller unstable with respect to symmetry lowering distortions, which transform as the five quadrupolar modes. The solution of the corresponding vibronic Hamiltonian is constructed using the analytical method introduced by Bargmann, as an alternative to existing group-theoretical methods based on coefficients of fractional parentage. It involves the construction of an Ansatz which incorporates SO(5) to SO(3) symmetry breaking. The resulting Jahn-Teller equations are derived, and solved in terms of radial polynomials and Gegenbauer functions.
Journal of the Chemical Society, Faraday Transactions, 1995
Euler's theorem is extended to the permutation symmetries of objects associated with vertices... more Euler's theorem is extended to the permutation symmetries of objects associated with vertices, edges and faces of general polyhedra imbedded in the sphere, torus or a surface of higher genus. An equivalent general theorem is derived for benzenoid hydrocarbons. Further relations are found for deltahedral and three-coordinate polyhedra imbedded in the various surfaces. Application of the new theorems to vibrational analysis and molecular electronic structure is sketched, with particular reference to bonding in possible toroidal analogues of the fullerenes.
Advances in Quantum Chemistry, 2003
ABSTRACT
The shell structure of matter is a unifying principle, from the fixed orbits of the planets, to t... more The shell structure of matter is a unifying principle, from the fixed orbits of the planets, to the gyrating electrons in an atom, and the dance of the quarks in protons and neutrons. It puts Mendeleev’s Periodic System, proposed 150 years ago, into the historical perspective of two other great taxonomies: the earlier planetary law of Titius-Bode, and the later quark hypothesis by Gell-Mann. In the case of the quarks, use was made of the theory of symmetry groups, which was created around 1830 in a flash of genius by Évariste Galois. Its subsequent application to the symmetry of continua is due to Sophus Lie. In this respect the classification of hadronic matter by group theory shows a more advanced and mature form of theory, as compared to the quantum mechanical treatment of the Periodic System. In 1969, at the centennial of Mendeleev’s discovery, Löwdin noted how remarkable it was that the periodicity of the table had not been derived from first principles. This challenge is calli...
Physical Review B, 1999
Effects of electron correlation, intrasite vibronic interaction, and merohedral disorder on the e... more Effects of electron correlation, intrasite vibronic interaction, and merohedral disorder on the electronic structure of K 4 C 60 are investigated with a model approach taking into account all essential interactions in the lowest unoccupied molecular orbital ͑LUMO͒ band. The self-energy was calculated within the GW approximation with self-consistency after the quasiparticle Green function starting from Hartree-Fock band structure. The insulating state arises due to interorbital charge disproportionation within the LUMO band while the band gap is strongly reduced by effects of long-range electron correlation. The results of the calculations are in reasonable agreement with experiment, providing evidence for a Jahn-Teller induced transition from a Mott-Hubbard to a band insulator state. ͓S0163-1829͑99͒51020-5͔
International Journal of Quantum Chemistry, 2018
A well defined class of planar or quasi-planar elongated boron clusters, of type B q− 7+3n , serv... more A well defined class of planar or quasi-planar elongated boron clusters, of type B q− 7+3n , serves as a basis to identify the valence bond picture of delocalized boron networks. The origin of the series is the B − 7 cluster, which exhibits σ-aromaticity. The cluster generating step is the repetitive expansion by three boron atoms in the direction of elongation. Specific electron counting rules are obtained for π-bonding, peripheral σ-bonding and multi-center inner σ-bonding. A valence bond structure is introduced which explains the remarkable regularity in the bonding pattern. The analysis supports 4c-2e bonds as an alternative to the common 3c-2e bonds. The results are validated by symmetry induction and ab initio calculations.
Physical Review B, 1996
The instability of a high-symmetry distribution of conduction electrons in t-type orbitals in cub... more The instability of a high-symmetry distribution of conduction electrons in t-type orbitals in cubic lattices is investigated within the mean-field approach. All essential bielectronic and one-site vibronic interactions involving the threefold degenerate orbitals are taken into account. It is shown that the degeneracy of the site orbitals may give rise to a special kind of electronic instability, described as orbital disproportionation of the conduction-electron density at each site. The criterion for instability of the cubic band structure with respect to a homogeneous disproportionation, including both spin-and charge-density redistributions, is established. Low-symmetry nuclear distortions may reinforce the tendency for disproportionation of charge density between t orbitals. A model calculation suggests that electronic charge disproportionation may be responsible for the unusual band structure of alkali-metal-doped fullerides. ͓S0163-1829͑96͒05423-9͔
Physical Chemistry Chemical Physics, 2018
Valence bonds within the perimeter of disk-like boron clusters with a concentric topology follow ... more Valence bonds within the perimeter of disk-like boron clusters with a concentric topology follow simple 4n and 8n electron counting rules.
AIP Conference Proceedings, 2000
The electronic structure of K3C60 is investigated in a band approach allowing for arbitrary distr... more The electronic structure of K3C60 is investigated in a band approach allowing for arbitrary distribution of the charge density among the three LUMO orbitals at each fullerene site (a model analogue of the LDA+U method). The predictions for optical absorption and EELS of these broken-symmetry band structure calculations are compared with available experimental data. We find that such calculations reproduce the three absorption bands in the low energy region of the optical conductivity spectrum and give the correct dc limit for the conductivity. Simulations of the loss function show the right position and width of the metallic plasmon peak. Similar calculations within the conventional band structure approach fail to reproduce the above spectroscopic features.
Journal of the Chemical Society, Faraday Transactions, 1995
Euler's theorem is extended to the permutation symmetries of objects associated with vertices... more Euler's theorem is extended to the permutation symmetries of objects associated with vertices, edges and faces of general polyhedra imbedded in the sphere, torus or a surface of higher genus. An equivalent general theorem is derived for benzenoid hydrocarbons. Further relations are found for deltahedral and three-coordinate polyhedra imbedded in the various surfaces. Application of the new theorems to vibrational analysis and molecular electronic structure is sketched, with particular reference to bonding in possible toroidal analogues of the fullerenes.
Journal of Physics A: Mathematical and Theoretical, 2017
The Bargmann-Fock representation of the Rabi Hamiltonian is expressed by a system of two coupled ... more The Bargmann-Fock representation of the Rabi Hamiltonian is expressed by a system of two coupled first-order differential equations in the complex field, which may be rewritten in a canonical form under the Birkhoff transformation. The transformation gives rise to leapfrog recurrence relations, from which the eigenvalues and eigenvectors could be obtained. The interesting feature of this approach is that it generates integer quantum numbers, which relate the solutions to the Juddian baselines. The relationship with Braak's integrability claim [PRL 107, 100401 (2011)] is discussed.