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Sousa C, Sánchez-Mansilla A, Broer R, Straatsma TP, de Graaf C. A Nonorthogonal Configuration Interaction Approach to Singlet Fission in Perylenediimide Compounds. J Phys Chem A 2023; 127:9944-9958. [PMID: 37964533 PMCID: PMC10694806 DOI: 10.1021/acs.jpca.3c04975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/07/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
Perylenediimide molecules constitute a family of chromophores that undergo singlet fission, a process in which an excited singlet state converts into lower energy triplets on two neighboring molecules, potentially increasing the efficiency of organic solar cells. Here, the nonorthogonal configuration interaction method is applied to study the effect of the different crystal packing of various perylenediimide derivatives on the relative energies of the singlet and triplet states, the intermolecular electronic couplings, and the relative rates for singlet fission. The analysis of the wave functions and electronic couplings reveals that charge transfer states play an important role in the singlet fission mechanism. Dimer conformations where the PDI molecules are at large displacements along the long axis and short on the short axis are posed as the most favorable for singlet fission. The role of the substituent at the imide group has been inspected concluding that, although it has no effect in the energies, for some conformations it significantly influences the electronic couplings, and therefore, replacing this substituent with hydrogen may introduce artifacts in the computational modeling of the PDI molecules.
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Affiliation(s)
- C. Sousa
- Departament
de Ciència de Materials i Química Física and
Institut de Química Teòrica i Computacional, Universitat de Barcelona, 08028 Barcelona, Spain
| | - A. Sánchez-Mansilla
- Departament
de Química Física i Inorgànica, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - R. Broer
- Zernike
Institute of Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
| | - T. P. Straatsma
- National
Center for Computational Sciences, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831-6373, United States
- Department
of Chemistry and Biochemistry, University
of Alabama, Tuscaloosa, Alabama 35487-0336, United States
| | - C. de Graaf
- Departament
de Química Física i Inorgànica, Universitat Rovira i Virgili, 43007 Tarragona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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Straatsma TP, Broer R, Sánchez-Mansilla A, Sousa C, de Graaf C. GronOR: Scalable and Accelerated Nonorthogonal Configuration Interaction for Molecular Fragment Wave Functions. J Chem Theory Comput 2022; 18:3549-3565. [PMID: 35640094 DOI: 10.1021/acs.jctc.2c00266] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
GronOR is a program package for nonorthogonal configuration interaction calculations. Electronic wave functions are constructed in terms of antisymmetrized products of multiconfiguration molecular fragment wave functions. The computational complexity of the nonorthogonal methodologies implemented in GronOR applied to large molecular assemblies requires a design that takes full advantage of massively parallel supercomputer architectures and accelerator technologies. This work describes the implementation strategy and resulting performance characteristics. In addition to parallelization and acceleration, the software development strategy includes aspects of fault resiliency and heterogeneous computing. The program was designed for large-scale supercomputers but also runs effectively on small clusters and workstations for small molecular systems. GronOR is available as open source to the scientific community.
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Affiliation(s)
- T P Straatsma
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6373, United States.,Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487-0336, United States
| | - R Broer
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - A Sánchez-Mansilla
- Department of Physical and Inorganic Chemistry, Universitat Rovira i Virgili, C. Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - C Sousa
- Department of Physical Chemistry and Institut de Química Teòrica i Computacional, Universitat de Barcelona, 08028 Barcelona, Spain
| | - C de Graaf
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.,Department of Physical and Inorganic Chemistry, Universitat Rovira i Virgili, C. Marcel·lí Domingo 1, 43007 Tarragona, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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Sánchez-Mansilla A, Sousa C, Kathir RK, Broer R, Straatsma TP, de Graaf C. On the role of dynamic electron correlation in non-orthogonal configuration interaction with fragments. Phys Chem Chem Phys 2022; 24:11931-11944. [PMID: 35521680 DOI: 10.1039/d2cp00772j] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two different approaches have been implemented to include the effect of dynamic electron correlation in the Non-Orthogonal Configuration Interaction for Fragments (NOCI-F) method. The first is based on shifting the diagonal matrix elements of the NOCI matrix, while the second incorporates the dynamic correlation explicitly in the fragment wave functions used to construct the many-electron basis functions of the NOCI. The two approaches are illustrated for the calculation of the electronic coupling relevant in singlet fission and the coupling of spin moments in organic radicals. Comparison of the calculated diabatic couplings, the NOCI energies and wave functions shows that dynamic electron correlation is not only efficiently but also effectively incorporated by the shifting approach and can largely affect the coupling between electronic states. Also, it brings the NOCI coupling of the spin moments in close agreement with benchmark calculations.
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Affiliation(s)
- A Sánchez-Mansilla
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
| | - C Sousa
- Departament de Ciència de Materials i Química Física and Institut de Química Teòrica i Computacional, Universitat de Barcelona, Spain.
| | - R K Kathir
- Zernike Institute of Advanced Materials, University of Groningen, The Netherlands
| | - R Broer
- Zernike Institute of Advanced Materials, University of Groningen, The Netherlands
| | - T P Straatsma
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6373, USA.,Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL 35487-0336, USA
| | - C de Graaf
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain.,Zernike Institute of Advanced Materials, University of Groningen, The Netherlands.,ICREA, Pg. Lluís Companys 23, Barcelona, Spain.
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Straatsma TP, Broer R, Faraji S, Havenith RWA, Suarez LEA, Kathir RK, Wibowo M, de Graaf C. GronOR: Massively parallel and GPU-accelerated non-orthogonal configuration interaction for large molecular systems. J Chem Phys 2020; 152:064111. [PMID: 32061226 DOI: 10.1063/1.5141358] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
GronOR is a program package for non-orthogonal configuration interaction calculations for an electronic wave function built in terms of anti-symmetrized products of multi-configuration molecular fragment wave functions. The two-electron integrals that have to be processed may be expressed in terms of atomic orbitals or in terms of an orbital basis determined from the molecular orbitals of the fragments. The code has been specifically designed for execution on distributed memory massively parallel and Graphics Processing Unit (GPU)-accelerated computer architectures, using an MPI+OpenACC/OpenMP programming approach. The task-based execution model used in the implementation allows for linear scaling with the number of nodes on the largest pre-exascale architectures available, provides hardware fault resiliency, and enables effective execution on systems with distinct central processing unit-only and GPU-accelerated partitions. The code interfaces with existing multi-configuration electronic structure codes that provide optimized molecular fragment orbitals, configuration interaction coefficients, and the required integrals. Algorithm and implementation details, parallel and accelerated performance benchmarks, and an analysis of the sensitivity of the accuracy of results and computational performance to thresholds used in the calculations are presented.
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Affiliation(s)
- T P Straatsma
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6373, USA
| | - R Broer
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - S Faraji
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - R W A Havenith
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - L E Aguilar Suarez
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - R K Kathir
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - M Wibowo
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - C de Graaf
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
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Abstract
First principles calculations in the framework of Density Functional Theory (DFT) and wavefunction-based correlated methods have been performed to investigate in detail the magnetic anisotropy in Sr3NiPtO6. This material is known for the easy-plane anisotropy with a large anisotropy constant of about 7.5-9.3 meV. We find that by properly choosing the onsite Coulomb repulsion and exchange parameters, DFT can correctly explain the easy-plane magnetocrystalline anisotropy of the material, but the magnitude of the anisotropy constant is underestimated. On the other hand, a quantitative agreement with respect to experiments, both in the magnitude and direction of the magnetic anisotropy, can be recovered by using the wavefunction-based approach which is able to fully describe the multiplet physics. We also show that the presence of structural distortions of the local NiO6 coordination is crucial for stabilizing the magnetic anisotropy in this compound.
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Affiliation(s)
- A-M Pradipto
- Consiglio Nazionale delle Ricerche - CNR-SPIN, I-66100 Chieti, Italy.
| | - R Broer
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.
| | - S Picozzi
- Consiglio Nazionale delle Ricerche - CNR-SPIN, I-66100 Chieti, Italy.
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Maurice R, Pradipto AM, Guihéry N, Broer R, de Graaf C. Antisymmetric Magnetic Interactions in Oxo-Bridged Copper(II) Bimetallic Systems. J Chem Theory Comput 2010; 6:3092-101. [DOI: 10.1021/ct100329n] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- R. Maurice
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse 3, 118, route de Narbonne, 31062 Toulouse France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo s/n, 43007 Tarragona, Spain, Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747AG, The Netherlands, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010, Barcelona, Spain
| | - A. M. Pradipto
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse 3, 118, route de Narbonne, 31062 Toulouse France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo s/n, 43007 Tarragona, Spain, Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747AG, The Netherlands, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010, Barcelona, Spain
| | - N. Guihéry
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse 3, 118, route de Narbonne, 31062 Toulouse France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo s/n, 43007 Tarragona, Spain, Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747AG, The Netherlands, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010, Barcelona, Spain
| | - R. Broer
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse 3, 118, route de Narbonne, 31062 Toulouse France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo s/n, 43007 Tarragona, Spain, Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747AG, The Netherlands, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010, Barcelona, Spain
| | - C. de Graaf
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse 3, 118, route de Narbonne, 31062 Toulouse France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo s/n, 43007 Tarragona, Spain, Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747AG, The Netherlands, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010, Barcelona, Spain
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Affiliation(s)
- R. Broer
- b Department of Chemical Physics , University of Groningen , Nijenborgh 16, 9747 , AG , Groningen , The Netherlands
| | - Inder P. Batra
- a IBM Research Laboratory , San Jose , California , 95193 , U.S.A
| | - P. S. Bagus
- a IBM Research Laboratory , San Jose , California , 95193 , U.S.A
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Affiliation(s)
- G. de Brouckère
- a Van der Walls Laboratory, University of Amsterdam , 67, Valckenierstraat, 1018 XE , Amsterdam , The Netherlands
| | - R. Broer
- b Theoretical Chemistry Group, Department of Chemistry , University of Groningen , Nijenborgh 16, 9747 AG , Groningen , The Netherlands
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Adamo C, Barone V, Bencini A, Broer R, Filatov M, Harrison NM, Illas F, Malrieu JP, Moreira IDPR. Comment on “About the calculation of exchange coupling constants using density-functional theory: The role of the self-interaction error” [J. Chem. Phys. 123, 164110 (2005)]. J Chem Phys 2006; 124:107101; author reply 107102. [PMID: 16542105 DOI: 10.1063/1.2178791] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
Magnetic interactions in ladder vanadates are determined with quantum chemical computational schemes using the embedded cluster model approach to represent the material. The available experimental data for calcium vanadate is accurately reproduced and the nature of the interladder interaction is established to be ferromagnetic. An analysis of the main contributions to the magnetic couplings is presented and the role of the covalently bonded apex oxygen is elucidated. In the sodium vanadate, the ground state configuration of the rungs is V-3d1-O-2p5-V-3d1. We show that with this configuration good intrachain coupling constants are obtained for the high-temperature phase. The interchain coupling in NaV2O5 is predicted to be approximately 34 K, ferromagnetic in nature.
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Affiliation(s)
- C de Graaf
- Department of Physical and Inorganic Chemistry, Universitat Rovira i Virgili, Placa Imperial Tarraco 1, 43005 Tarragona, Spain.
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Hozoi L, de Vries AH, van Oosten AB, Broer R, Cabrero J, de Graaf C. Theoretical characterization of the ground and optically excited states of alpha'-NaV2O5. Phys Rev Lett 2002; 89:076407. [PMID: 12190542 DOI: 10.1103/physrevlett.89.076407] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2002] [Indexed: 05/23/2023]
Abstract
The character of the ground and optically excited states was investigated by quantum chemical calculations. We propose a rung ground state with V 3d(1)(xy)-O 2p(1)(y)-V 3d(1)(xy) character, instead of the conventional picture of one unpaired electron shared by 2 V ions. The unpaired electron on O is low-spin coupled to the V d electrons and spin density is predicted to be localized on vanadium. The absorption peak at 0.9 eV is assigned to a state with similar orbital occupations but a different spin coupling scheme, resulting in spin density localized on the bridging oxygen.
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Affiliation(s)
- L Hozoi
- Theoretical Chemistry and Materials Science Centre, Rijksuniversiteit Groningen, Nijenborgh 4, The Netherlands
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Bagus PS, Broer R, de Jong WA, Nieuwpoort WC, Parmigiani F, Sangaletti L. Atomic many-body effects for the p-shell photoelectron spectra of transition metals. Phys Rev Lett 2000; 84:2259-2262. [PMID: 11017258 DOI: 10.1103/physrevlett.84.2259] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/1999] [Indexed: 05/23/2023]
Abstract
Ab initio theoretical results for the 2p- and 3p-hole states of an Mn(2+) ion are reported in order to determine the importance of atomic contributions to the photoelectron spectra of bulk MnO. A combined treatment of relativity and electron correlation reveals important physical effects that have been neglected in virtually all previous work. The many-body and relativistic effects included in the atomic model are able, without any ad hoc empirical parameters, to explain most of the features of the MnO photoelectron spectra. In particular, it is not necessary to invoke charge transfer to explain the complex p-level spectra.
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Affiliation(s)
- P S Bagus
- Department of Chemistry, Texas A&M University, College Station, Texas 77842-3012, USA
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Pernpointner M, Visscher L, de Jong WA, Broer R. Parallelization of four-component calculations. I. Integral generation, SCF, and four-index transformation in the Dirac-Fock package MOLFDIR. J Comput Chem 2000. [DOI: 10.1002/1096-987x(200010)21:13<1176::aid-jcc6>3.0.co;2-e] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Broer R, Heldens JG, van Strien EA, Zuidema D, Vlak JM. Specificity of multiple homologous genomic regions in Spodoptera exigua nucleopolyhedrovirus DNA replication. J Gen Virol 1998; 79 ( Pt 6):1563-72. [PMID: 9634102 DOI: 10.1099/0022-1317-79-6-1563] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The region upstream of the Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV) ubiquitin gene contains four near-identical 68-bp-long palindromic repeats. This region, named Sehr6 and located at map unit (m.u.) 88 of the SeMNPV genome on pSeEcoRI-2.2, showed structural homology to previously identified homologous regions (hrs) in a number of other baculoviruses. Hrs function as enhancers of transcription and as putative origins (oris) of baculovirus DNA replication. Five additional hrs (Sehr1-Sehr5) were identified on the SeMNPV genome by Southern blot hybridization with an 18-bp-long oligonucleotide complementary to a sequence conserved within the arms of the four palindromic repeats of Sehr6. Sehr1-Sehr6 were dispersed on the SeMNPV genome at m.u. 8.0, 30.0, 38.5, 51.0, 77.0 and 88.0, respectively. Sequence analysis of these hrs confirmed the presence of palindromic repeats, highly similar to those found in pSeEcoRI-2.2. The number of palindromes varied from one (Sehr4) to nine (Sehr1) per hr. The Sehrs are all present in non-coding regions of the SeMNPV genome and also contain multiple putative transcription recognition sequences. Plasmids containing either of the Sehrs replicated in an SeMNPV-dependent DNA replication assay. The Sehrs were unable to replicate in an AcMNPV-dependent DNA replication assay. This was in contrast to the previously observed SeMNPV non-hr type ori, which replicated in the presence of both AcMNPV and SeMNPV. These data suggest that the replication of SeMNPV and the role of hrs in this process is highly specific.
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Affiliation(s)
- R Broer
- Department of Virology, Wageningen Agricultural University, The Netherlands
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Heldens JG, Broer R, Zuidema D, Goldbach RW, Vlak JM. Identification and functional analysis of a non-hr origin of DNA replication in the genome of Spodoptera exigua multicapsid nucleopolyhedrovirus. J Gen Virol 1997; 78 ( Pt 6):1497-506. [PMID: 9191948 DOI: 10.1099/0022-1317-78-6-1497] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The genome of Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV) was screened for the presence of putative origins of DNA replication (oris). Using a transient DNA replication assay, several fragments were identified that underwent SeMNPV-dependent DNA replication in Spodoptera frugiperda cells (Sf-AE-21). Preliminary sequence data revealed the presence of multiple copies of homologous repeats (hrs). Restriction fragment Xbal-F2 showed a distinct sequence reminiscent of Autographa californica and Orgyla pseudotsugata MNPV (AcMNPV and OpMNPV) non-hr oris. Deletion analysis of this fragment indicated that the essential sequences of this putative non-hr ori mapped within a region of 800 bp. Sequence analysis of this region showed a unique distribution of six different (im)-perfect palindromes, several polyadenylation motifs and the occurrence of multiple direct repeats. No sequence homology or similarities to other reported baculovirus oris were detected. The spatial and modular distribution of these motifs are similar to those of the non-hr oris of AcMNPV and OpMNPV. Comparison of baculovirus non-hr and consensus eukaryotic oris revealed no consensus ori but indicated that each of the non-hrs studied so far is unique. From the structural similarity, however, it was concluded that the SeMNPV Xbal-F2 ori represents a baculovirus non-hr type ori. In addition, evidence is provided that SeMNPV renders more specificity to baculovirus DNA replication than AcMNPV.
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Affiliation(s)
- J G Heldens
- Department of Virology, Wageningen Agricultural University, The Netherlands
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Sousa C, de Jong WA, Broer R, Nieuwpoort WC. Theoretical characterization of the low-lying excited states of the CuCl molecule. J Chem Phys 1997. [DOI: 10.1063/1.473161] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Hu ZH, Broer R, Westerlaken J, Martens JW, Jin F, Jehle JA, Wang LM, Vlak JM. Characterization of the ecdysteroid UDP-glucosyltransferase gene of a single nucleocapsid nucleopolyhedrovirus of Buzura suppressaria. Virus Res 1997; 47:91-7. [PMID: 9037741 DOI: 10.1016/s0168-1702(96)01406-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A putative ecdysteroid UDP-glucosyltransferase (egt) gene was identified in the single nucleocapsid nucleopolyhedrovirus of Buzura suppressaria (BusuNPV). This is the first egt gene to be characterized in a SNPV, suggesting that egt genes are prevalent in nucleopolyhedroviruses and possibly in all baculoviruses. The open reading frame (ORF) of the gene is 1539 nucleotides (nt) long, encoding a putative protein (EGT) of 513 amino acids (aa) with a M of 58922. The 5' noncoding region contains three possible TATA boxes. A polyadenylation signal, AATAAA, was found downstream of the translation stop codon. A putative signal peptide of 16 residues was present at the N-terminus of the EGT. The BusuNPV egt gene has a high degree of nucleotide and amino acid sequence homology to multiple nucleocapsid (M) NPV egt genes, the highest being to the Spodoptera exigua MNPV egt. A phylogenetic tree of eleven known EGTs was constructed using maximum parsimony analysis.
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Affiliation(s)
- Z H Hu
- Department of Virology, Wageningen Agricultural University, Netherlands
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van Poelwijk F, Broer R, Belsham GJ, Oudshoorn P, Vlak JM, Goldbach RW. A hybrid baculovirus-bacteriophage T7 transient expression system. Biotechnology (N Y) 1995; 13:261-4. [PMID: 9634768 DOI: 10.1038/nbt0395-261] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A hybrid recombinant baculovirus-bacteriophage T7 expression system was developed for transient expression in insect cells of plasmids with foreign genes provided with a T7 promoter. The coding sequence for T7 RNA polymerase, with or without a nuclear localization signal, was inserted into the genome of Autographa californica nuclear polyhedrosis virus. Recombinant viruses stably expressed T7 RNA polymerase in insect cells. Upon transfection of infected insect cells with plasmids containing the genes for chloramphenicol acetyltransferase (CAT), the hepatitis B virus precore-, core- or e- antigens under control of the T7 promoter, transient expression of these genes was detected by ELISA. The results obtained indicate that this baculovirus/T7 system provides a simple and widely applicable tool for transient gene expression studies.
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Kool M, Broer R, Zuidema D, Goldbach RW, Vlak JM. Nucleotide sequence and genetic organization of a 7.3 kb region (map unit 47 to 52.5) of Autographa californica nuclear polyhedrosis virus fragment EcoRI-C. J Gen Virol 1994; 75 ( Pt 3):487-94. [PMID: 8126447 DOI: 10.1099/0022-1317-75-3-487] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The nucleotide sequence and genetic organization of a 7297 bp region within the EcoRI-C fragment of Autographa californica multiple nucleocapsid nuclear polyhedrosis virus (AcMNPV) are presented. Eight putative open reading frames were found and their respective amino acid sequences compared with a number of data libraries. ORF 1227 corresponded with gp41 and its predicted protein sequence was found to be 55 amino acids longer at its C terminus than reported previously. Moreover the main part of the ORF 1227 product, including the additional 55 amino acids, showed a high degree of homology with protein p40 of Helicoverpa zea single nucleocapsid nuclear polyhedrosis virus (HzSNPV). Three other ORFs in the analysed AcMNPV region showed homology with ORFs in the HzSNPV sequence, indicating that the general organization of this region is similar in both viruses. However one ORF found in the AcMNPV sequence was absent from the corresponding HzSNPV sequence.
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Affiliation(s)
- M Kool
- Department of Virology, Wageningen Agricultural University, The Netherlands
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Abstract
To study the function of the envelope glycoprotein gH of pseudorabies virus, a gH null mutant was constructed. A premature translation termination codon was introduced in the gH gene by linker insertion mutagenesis, and a mutant virus was rescued by using a cell line that expresses the wild-type protein. Mutant virus isolated from complementing cells was unable to form plaques on noncomplementing cells, indicating that gH is essential in the life cycle of the virus. Immunological staining and electron microscopy showed that the mutant virus produced noninfectious progeny and was unable to spread from infected to uninfected cells by cell-cell fusion. Thus, similar to gH of herpes simplex virus, gH of pseudorabies virus is required for entry and cell-to-cell spread.
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Affiliation(s)
- B Peeters
- Virology Department, Central Veterinary Institute, Lelystad, The Netherlands
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Broer R, Nieuwpoort WC. Broken orbital symmetry and the description of valence hole states in the tetrahedral [CrO4]2? anion. ACTA ACUST UNITED AC 1988. [DOI: 10.1007/bf00527744] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Broer R, Nieuwpoort W. Broken orbital-symmetry and the description of hole states in the tetrahedral [CrO4]− anion. I. Introductory considerations and calculations on oxygen 1s hole states. Chem Phys 1981. [DOI: 10.1016/0301-0104(81)85107-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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