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Author

Martin J. Packer

Other affiliations: University of Southern Denmark
Bio: Martin J. Packer is an academic researcher from University of Sheffield. The author has contributed to research in topics: Proton NMR & Chemistry. The author has an hindex of 17, co-authored 27 publications receiving 2929 citations. Previous affiliations of Martin J. Packer include University of Southern Denmark.
Topics: Proton NMR, Chemistry, PARP1, Ab initio, Pharmacology

Papers
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Journal ArticleDOI
Kestutis Aidas1, Celestino Angeli2, Keld L. Bak3, Vebjørn Bakken4, Radovan Bast5, Linus Boman6, Ove Christiansen3, Renzo Cimiraglia2, Sonja Coriani7, Pål Dahle8, Erik K. Dalskov, Ulf Ekström4, Thomas Enevoldsen9, Janus J. Eriksen3, Patrick Ettenhuber3, Berta Fernández10, Lara Ferrighi, Heike Fliegl4, Luca Frediani, Kasper Hald11, Asger Halkier, Christof Hättig12, Hanne Heiberg13, Trygve Helgaker4, Alf C. Hennum14, Hinne Hettema15, Eirik Hjertenæs16, Stine Høst3, Ida-Marie Høyvik3, Maria Francesca Iozzi17, Brannislav Jansik18, Hans-Jørgen Aa. Jensen9, Dan Jonsson, Poul Jørgensen3, Johanna Kauczor19, Sheela Kirpekar, Thomas Kjærgaard3, Wim Klopper20, Stefan Knecht21, Rika Kobayashi22, Henrik Koch16, Jacob Kongsted9, Andreas Krapp, Kasper Kristensen3, Andrea Ligabue23, Ola B. Lutnæs24, Juan Ignacio Melo25, Kurt V. Mikkelsen26, Rolf H. Myhre16, Christian Neiss27, Christian B. Nielsen, Patrick Norman19, Jeppe Olsen3, Jógvan Magnus Haugaard Olsen9, Anders Osted, Martin J. Packer9, Filip Pawłowski28, Thomas Bondo Pedersen4, Patricio Federico Provasi29, Simen Reine4, Zilvinas Rinkevicius5, Torgeir A. Ruden, Kenneth Ruud, Vladimir V. Rybkin20, Paweł Sałek, Claire C. M. Samson20, Alfredo Sánchez de Merás30, Trond Saue31, Stephan P. A. Sauer26, Bernd Schimmelpfennig20, Kristian Sneskov11, Arnfinn Hykkerud Steindal, Kristian O. Sylvester-Hvid, Peter R. Taylor32, Andrew M. Teale33, Erik I. Tellgren4, David P. Tew34, Andreas J. Thorvaldsen3, Lea Thøgersen35, Olav Vahtras5, Mark A. Watson36, David J. D. Wilson37, Marcin Ziółkowski38, Hans Ågren5 
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

Journal ArticleDOI
TL;DR: In this article, the potential energy surface for dinucleotide steps in double helical DNA was calculated as a function of the two principal degrees of freedom, slide and shift, using a virtual bond to model the constraints imposed by the sugar-phosphate backbone.

226 citations

Journal ArticleDOI
TL;DR: In this paper, a new implementation of the second-order polarization propagator approximation (SOPPA) using a direct linear transformation approach is presented, in which the SOPPA equations are solved iteratively.
Abstract: We present a new implementation of the second‐order polarization propagator approximation (SOPPA) using a direct linear transformation approach, in which the SOPPA equations are solved iteratively. This approach has two important advantages over its predecessors. First, the direct linear transformation allows for more efficient calculations for large two particle–two hole excitation manifolds. Second, the operation count for SOPPA is lowered by one order, to N5. As an application of the new implementation, we calculate the excitation energies and oscillator strengths of the lowest singlet and triplet transitions for benzene and naphthalene. The results compare well with experiment and CASPT2 values, calculated with identical basis sets and molecular geometries. This indicates that SOPPA can provide reliable values for excitation energies and response properties for relatively large molecular systems.

167 citations


Cited by
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Journal ArticleDOI
TL;DR: Some recent examples where dynamic covalent chemistry has been demonstrated are shown to emphasise the basic concepts of this area of science.
Abstract: Dynamic covalent chemistry relates to chemical reactions carried out reversibly under conditions of equilibrium control. The reversible nature of the reactions introduces the prospects of "error checking" and "proof-reading" into synthetic processes where dynamic covalent chemistry operates. Since the formation of products occurs under thermodynamic control, product distributions depend only on the relative stabilities of the final products. In kinetically controlled reactions, however, it is the free energy differences between the transition states leading to the products that determines their relative proportions. Supramolecular chemistry has had a huge impact on synthesis at two levels: one is noncovalent synthesis, or strict self-assembly, and the other is supramolecular assistance to molecular synthesis, also referred to as self-assembly followed by covalent modification. Noncovalent synthesis has given us access to finite supermolecules and infinite supramolecular arrays. Supramolecular assistance to covalent synthesis has been exploited in the construction of more-complex systems, such as interlocked molecular compounds (for example, catenanes and rotaxanes) as well as container molecules (molecular capsules). The appealing prospect of also synthesizing these types of compounds with complex molecular architectures using reversible covalent bond forming chemistry has led to the development of dynamic covalent chemistry. Historically, dynamic covalent chemistry has played a central role in the development of conformational analysis by opening up the possibility to be able to equilibrate configurational isomers, sometimes with base (for example, esters) and sometimes with acid (for example, acetals). These stereochemical "balancing acts" revealed another major advantage that dynamic covalent chemistry offers the chemist, which is not so easily accessible in the kinetically controlled regime: the ability to re-adjust the product distribution of a reaction, even once the initial products have been formed, by changing the reaction's environment (for example, concentration, temperature, presence or absence of a template). This highly transparent, yet tremendously subtle, characteristic of dynamic covalent chemistry has led to key discoveries in polymer chemistry. In this review, some recent examples where dynamic covalent chemistry has been demonstrated are shown to emphasise the basic concepts of this area of science.

1,880 citations

Book ChapterDOI
TL;DR: The chapter focuses on a general description of the force fields that are most commonly used at present and gives an indication of the directions of current research that may yield better functions in the near future.
Abstract: Publisher Summary The chapter focuses on a general description of the force fields that are most commonly used at present, and it gives an indication of the directions of current research that may yield better functions in the near future. After a brief survey of current models, mostly generated during the 1990s, the focus of the chapter is on the general directions the field is taking in developing new models. The most commonly used protein force fields incorporate a relatively simple potential energy function: The emphasis is on the use of continuum methods to model the electrostatic effects of hydration and the introduction of polarizability to model the electronic response to changes in the environment. Some of the history and performance of widely used protein force fields based on an equation on simplest potential energy function or closely related equations are reviewed. The chapter outlines some promising developments that go beyond this, primarily by altering the way electrostatic interactions are treated. The use of atomic multipoles and off-center charge distributions, as well as attempts to incorporate electronic polarizability, are also discussed in the chapter.

1,743 citations

Journal Article
TL;DR: In this article, a nucleosome-DNA interaction model was proposed to predict the genome-wide organization of nucleosomes, and it was shown that genomes encode an intrinsic nucleosomal organization and that this intrinsic organization can explain ∼50% of the in-vivo positions.
Abstract: Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome–DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain ∼50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.

1,399 citations

Journal ArticleDOI
08 May 2003-Nature
TL;DR: Comparison of the 147-base-pair structure with two 146- base-pair structures reveals alterations in DNA twist that are evidently common in bulk chromatin, and which are of probable importance for chromatin fibre formation and chromatin remodelling.
Abstract: The 1.9-A-resolution crystal structure of the nucleosome core particle containing 147 DNA base pairs reveals the conformation of nucleosomal DNA with unprecedented accuracy. The DNA structure is remarkably different from that in oligonucleotides and non-histone protein-DNA complexes. The DNA base-pair-step geometry has, overall, twice the curvature necessary to accommodate the DNA superhelical path in the nucleosome. DNA segments bent into the minor groove are either kinked or alternately shifted. The unusual DNA conformational parameters induced by the binding of histone protein have implications for sequence-dependent protein recognition and nucleosome positioning and mobility. Comparison of the 147-base-pair structure with two 146-base-pair structures reveals alterations in DNA twist that are evidently common in bulk chromatin, and which are of probable importance for chromatin fibre formation and chromatin remodelling.

1,250 citations

Journal ArticleDOI
Kestutis Aidas1, Celestino Angeli2, Keld L. Bak3, Vebjørn Bakken4, Radovan Bast5, Linus Boman6, Ove Christiansen3, Renzo Cimiraglia2, Sonja Coriani7, Pål Dahle8, Erik K. Dalskov, Ulf Ekström4, Thomas Enevoldsen9, Janus J. Eriksen3, Patrick Ettenhuber3, Berta Fernández10, Lara Ferrighi, Heike Fliegl4, Luca Frediani, Kasper Hald11, Asger Halkier, Christof Hättig12, Hanne Heiberg13, Trygve Helgaker4, Alf C. Hennum14, Hinne Hettema15, Eirik Hjertenæs16, Stine Høst3, Ida-Marie Høyvik3, Maria Francesca Iozzi17, Brannislav Jansik18, Hans-Jørgen Aa. Jensen9, Dan Jonsson, Poul Jørgensen3, Johanna Kauczor19, Sheela Kirpekar, Thomas Kjærgaard3, Wim Klopper20, Stefan Knecht21, Rika Kobayashi22, Henrik Koch16, Jacob Kongsted9, Andreas Krapp, Kasper Kristensen3, Andrea Ligabue23, Ola B. Lutnæs24, Juan Ignacio Melo25, Kurt V. Mikkelsen26, Rolf H. Myhre16, Christian Neiss27, Christian B. Nielsen, Patrick Norman19, Jeppe Olsen3, Jógvan Magnus Haugaard Olsen9, Anders Osted, Martin J. Packer9, Filip Pawłowski28, Thomas Bondo Pedersen4, Patricio Federico Provasi29, Simen Reine4, Zilvinas Rinkevicius5, Torgeir A. Ruden, Kenneth Ruud, Vladimir V. Rybkin20, Paweł Sałek, Claire C. M. Samson20, Alfredo Sánchez de Merás30, Trond Saue31, Stephan P. A. Sauer26, Bernd Schimmelpfennig20, Kristian Sneskov11, Arnfinn Hykkerud Steindal, Kristian O. Sylvester-Hvid, Peter R. Taylor32, Andrew M. Teale33, Erik I. Tellgren4, David P. Tew34, Andreas J. Thorvaldsen3, Lea Thøgersen35, Olav Vahtras5, Mark A. Watson36, David J. D. Wilson37, Marcin Ziółkowski38, Hans Ågren5 
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