Computational Chemistry | Lund University Publications

Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks Ekberg, Vilhelm ^LU ; L. Samways, Marley ; Misini Ignjatović, Majda ^LU ; W. Essex, Jonathan and Ryde, Ulf ^LU

(2022) In ACS Physical Chemistry Au 2(3). p.247-259

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Self-Interactions of Two Monoclonal Antibodies : Small-Angle X-ray Scattering, Light Scattering, and Coarse-Grained Modeling Mahapatra, Sujata ; Polimeni, Marco ^LU ; Gentiluomo, Lorenzo ; Roessner, Dierk ; Frieß, Wolfgang ; Peters, Günther H. J. ; Streicher, Werner W. ; Lund, Mikael ^LU

and Harris, Pernille (2022) In Molecular Pharmaceutics 19(2). p.508-519

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The influence of hydrodynamic damping on the motion of an immersed elastic cantilever Lorentzon, J. ^LU ; Revstedt, J. ^LU and Austrell, P.E. ^LU (2022) In European Journal of Mechanics B - Fluids 95.

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Convergence of Electronic Structure Properties in Ionic Oxides Within a Fragment Approach Larsson, Ernst D. ^LU and Veryazov, Valera ^LU

(2022) In Frontiers in Chemistry 10.

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A program system for self-consistent embedded potentials for ionic crystals Larsson, Ernst D. ^LU ; Krośnicki, Marek and Veryazov, Valera ^LU

(2022) In Chemical Physics 562.

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Dip-and-pull ambient pressure photoelectron spectroscopy as a spectroelectrochemistry tool for probing molecular redox processes Temperton, Robert H. ^LU ; Kawde, Anurag ^LU ; Eriksson, Axl ^LU ; Wang, Weijia ^LU ; Kokkonen, Esko ^LU

; Jones, Rosemary ^LU ; Gericke, Sabrina Maria ^LU ; Zhu, Suyun ^LU ; Quevedo, Wilson and Seidel, Robert , et al. (2022) In Journal of Chemical Physics 157(24).

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Hybrids between Rubus caesius and Rubus sect. Corylifolii (Rosaceae) and their relation to R. cyclomorphus, R. tiliaster, R. glauciformis, R. slesvicensis and R. firmus Lewin, Marcus ; Zhou, Mingyue ; Montes, Melanie S. ; Mattsson, Tore ; Burén, Tomas ; Hedrén, Mikael ^LU and Ryde, Ulf ^LU

(2022) In Nordic Journal of Botany 2022(12).

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Unraveling the Reaction Mechanism of Mo/Cu CO Dehydrogenase Using QM/MM Calculations Ritacca, Alessandra G. ; Rovaletti, Anna ; Moro, Giorgio ; Cosentino, Ugo ; Ryde, Ulf ^LU

; Sicilia, Emilia and Greco, Claudio ^LU (2022) In ACS Catalysis 12(12). p.7336-7343

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Photophysical Integrity of the Iron(III) Scorpionate Framework in Iron(III)-NHC Complexes with Long-Lived ²LMCT Excited States Prakash, Om ^LU ; Lindh, Linnea ^LU

; Kaul, Nidhi ; Rosemann, Nils W. ^LU ; Losada, Iria Bolaño ^LU ; Johnson, Catherine ; Chábera, Pavel ^LU ; Ilic, Aleksandra ^LU

; Schwarz, Jesper ^LU and Gupta, Arvind Kumar ^LU , et al. (2022) In Inorganic Chemistry 61(44). p.17515-17526

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QM/MM Study of Partial Dissociation of S2B for the E₂ Intermediate of Nitrogenase Jiang, Hao ^LU

; Svensson, Oskar K. G. ^LU and Ryde, Ulf ^LU

(2022) In Inorganic Chemistry 61(45). p.18067-18076

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Assessing the structural and dynamical properties of concentrated solutions of the disordered proteins Histatin 5 and its tandem repeat Fagerberg, Eric ^LU (2022)

Thesis › Doctoral thesis (compilation)

On stability and relaxation techniques for partitioned fluid-structure interaction simulations Lorentzon, Johan ^LU and Revstedt, Johan ^LU (2022) In Engineering Reports 4(10).

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Photofunctionality of iron(III) N-heterocyclic carbenes and related d⁵ transition metal complexes Chábera, Pavel ^LU ; Lindh, Linnea ^LU

; Rosemann, Nils W. ^LU ; Prakash, Om ^LU ; Uhlig, Jens ^LU ; Yartsev, Arkady ^LU

; Wärnmark, Kenneth ^LU ; Sundström, Villy ^LU and Persson, Petter ^LU (2021) In Coordination Chemistry Reviews 426.

Contribution to journal › Scientific review

Building polymer-like clusters from colloidal particles with isotropic interactions, in aqueous solution Haddadi, Sara ^LU ; Skepö, Marie ^LU ; Jannasch, Patric ^LU

; Manner, Sophie ^LU and Forsman, Jan ^LU (2021) In Journal of Colloid and Interface Science 581. p.669-681

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Fighting microbial infections with force fields: Evaluating conformational ensembles of intrinsically disordered proteins Jephthah, Stephanie ^LU (2021)

Thesis › Doctoral thesis (compilation)

Quantum-refinement studies of the bidentate ligand of V‑nitrogenase and the protonation state of CO-inhibited Mo‑nitrogenase Bergmann, Justin ^LU ; Oksanen, Esko ^LU and Ryde, Ulf ^LU

(2021) In Journal of Inorganic Biochemistry 219.

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Critical evaluation of a crystal structure of nitrogenase with bound N₂ ligands Bergmann, Justin ^LU ; Oksanen, Esko ^LU and Ryde, Ulf ^LU

(2021) In Journal of Biological Inorganic Chemistry 26(2-3). p.341-353

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Impact of arginine−phosphate interactions on the reentrant condensation of disordered proteins Lenton, Samuel ^LU ; Hervø-Hansen, Stefan ^LU ; Popov, Anton M. ; Tully, Mark D. ; Lund, Mikael ^LU

and Skepö, Marie ^LU (2021) In Biomacromolecules 22(4). p.1532-1544

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Hybrids between Rubus idaeus and Rubus sect. Corylifolii and their relation to R. pruinosus and R. rosanthus Ryde, Ulf ^LU

; Montes, Melanie S. ; Zhou, Mingyue ; Mattsson, Tore ; Burén, Tomas and Hedrén, Mikael ^LU (2021) In Nordic Journal of Botany 39(8).

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Direct Evidence for Reaction between Cellulose and CO₂from Nuclear Magnetic Resonance Gunnarsson, Maria ^LU ; Bernin, Diana ; Hasani, Merima ; Lund, Mikael ^LU

and Bialik, Erik ^LU (2021) In ACS Sustainable Chemistry and Engineering 9(42). p.14006-14011

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Charge Regulation during Amyloid Formation of α-Synuclein Pálmadóttir, Tinna ^LU ; Malmendal, Anders ^LU ; Leiding, Thom ^LU ; Lund, Mikael ^LU

and Linse, Sara ^LU (2021) In Journal of the American Chemical Society 143(20). p.7777-7791

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Phase Transitions of Oppositely Charged Colloidal Particles Driven by Alternating Current Electric Field Li, Bin ^LU ; Wang, Yong Lei ; Shi, Guang ; Gao, Yangyang ; Shi, Xinghua ; Woodward, Clifford E. and Forsman, Jan ^LU (2021) In ACS Nano 15(2). p.2363-2373

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On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies Ekberg, Vilhelm ^LU and Ryde, Ulf ^LU

(2021) In Journal of Chemical Theory and Computation 17(8). p.5379-5391

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Resonant X-ray photo-oxidation of light-harvesting iron (II/III) N-heterocyclic carbene complexes Temperton, Robert H. ^LU ; Guo, Meiyuan ^LU ; D’Acunto, Giulio ^LU ; Johansson, Niclas ^LU ; Rosemann, Nils W. ^LU ; Prakash, Om ^LU ; Wärnmark, Kenneth ^LU ; Schnadt, Joachim ^LU

; Uhlig, Jens ^LU and Persson, Petter ^LU (2021) In Scientific Reports 11(1).

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Directional shear jamming of frictionless ellipses Trulsson, Martin ^LU

(2021) In Physical Review E 104(4).

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The effect of multisite phosphorylation on the conformational properties of intrinsically disordered proteins Rieloff, Ellen ^LU and Skepö, Marie ^LU (2021) In International Journal of Molecular Sciences 22(20).

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Comparison of the accuracy of DFT methods for reactions with relevance to nitrogenase Torbjörnsson, Magne ^LU and Ryde, Ulf ^LU

(2021) In Electronic Structure 3(3).

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From Attraction to Repulsion to Attraction: Non-Monotonic Temperature Dependence of Polymer-Mediated Interactions in Colloidal Dispersions Haddadi, Sara ^LU ; Skepö, Marie ^LU and Forsman, Jan ^LU (2021) In ACS Nanoscience AU 1(1). p.69-80

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Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity Jephthah, Stephanie ^LU ; Pesce, Francesco ; Lindorff-Larsen, Kresten and Skepö, Marie ^LU (2021) In Journal of Chemical Theory and Computation 17(10). p.6634-6646

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PED in 2021 : A major update of the protein ensemble database for intrinsically disordered proteins Lazar, Tamas ; Martínez-Pérez, Elizabeth ; Quaglia, Federica ; Hatos, András ; Chemes, Lucía B. ; Iserte, Javier A. ; Méndez, Nicolás A. ; Garrone, Nicolás A. ; Saldaño, Tadeo E. and Marchetti, Julia , et al. (2021) In Nucleic Acids Research 49(D1). p.404-411

Contribution to journal › Article

QM/MM study of the binding of H₂ to MoCu CO dehydrogenase : development and applications of improved H₂ van der Waals parameters Rovaletti, Anna ; Greco, Claudio ^LU and Ryde, Ulf ^LU

(2021) In Journal of Molecular Modeling 27(3).

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Estimating the accuracy of calculated electron paramagnetic resonance hyperfine couplings for a lytic polysaccharide monooxygenase Theibich, Yusuf A. ; Sauer, Stephan P.A. ; Leggio, Leila Lo and Hedegård, Erik D. ^LU (2021) In Computational and Structural Biotechnology Journal 19. p.555-567

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Microsecond Photoluminescence and Photoreactivity of a Metal-Centered Excited State in a Hexacarbene-Co(III) Complex Kaufhold, Simon ^LU

; Rosemann, Nils W. ^LU ; Chábera, Pavel ^LU ; Lindh, Linnea ^LU

; Bolanõ Losada, Iria ^LU ; Uhlig, Jens ^LU ; Pascher, Torbjörn ^LU ; Strand, Daniel ^LU ; Wärnmark, Kenneth ^LU and Yartsev, Arkady ^LU

, et al. (2021) In Journal of the American Chemical Society p.1307-1312

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Engineering the Oxidative Potency of Non-Heme Iron(IV) Oxo Complexes in Water for C-H Oxidation by a cis Donor and Variation of the Second Coordination Sphere Wegeberg, Christina ; Skavenborg, Mathias L. ; Liberato, Andrea ; McPherson, James N. ; Browne, Wesley R. ; Hedegård, Erik D. ^LU and McKenzie, Christine J. (2021) In Inorganic Chemistry 60(3). p.1975-1984

Contribution to journal › Article

The role of the active site tyrosine in the mechanism of lytic polysaccharide monooxygenase Mcevoy, Aina ; Creutzberg, Joel ^LU ; Singh, Raushan K. ; Bjerrum, Morten J. and Hedegård, Erik D. ^LU (2021) In Chemical Science 12(1). p.352-362

Contribution to journal › Article

Two-Substrate Glyoxalase i Mechanism : A Quantum Mechanics/Molecular Mechanics Study Jafari, Sonia ; Ryde, Ulf ^LU

and Irani, Mehdi ^LU (2021) In Inorganic Chemistry p.303-314

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Molecular dynamics simulations of phosphorylated intrinsically disordered proteins : A force field comparison Rieloff, Ellen ^LU and Skepö, Marie ^LU (2021) In International Journal of Molecular Sciences 22(18).

Contribution to journal › Article

Coarse-grained and atomistic modelling of phosphorylated intrinsically disordered proteins Rieloff, Ellen ^LU (2021)

Thesis › Doctoral thesis (compilation)

Oxygen chemistry of halogen-doped CeO₂(111) Wolf, Matthew J. ; Larsson, Ernst D. ^LU and Hermansson, Kersti (2021) In Physical Chemistry Chemical Physics 23(35). p.19375-19385

Contribution to journal › Article

On the Thermodynamic Solvation of Biomolecules in Solution Hervö Hansen, Stefan ^LU (2021)

Thesis › Doctoral thesis (compilation)

QM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues Jafari, Sonia ; Ryde, Ulf ^LU

and Irani, Mehdi ^LU (2021) In Journal of Chemical Theory and Computation 17(3). p.1822-1841

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Confinement-induced fluid-fluid phase transitions in simple fluid mixtures, under bulk supra-critical conditions Haddadi, Sara ^LU ; Woodward, Clifford E. and Forsman, Jan ^LU (2021) In Fluid Phase Equilibria 540.

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Structural transitions at electrodes, immersed in simple ionic liquid models Lu, Hongduo ^LU ; Stenberg, Samuel ^LU ; Woodward, Clifford E. and Forsman, Jan ^LU (2021) In Soft Matter 17(14). p.3876-3885

Contribution to journal › Article

Design of robust 2,2′-bipyridine ligand linkers for the stable immobilization of molecular catalysts on silicon(111) surfaces Johnson, Samantha ; Blakemore, James D. ; Brunschwig, Bruce S. ; Lewis, Nathan S. ; Gray, Harry B. ; Goddard, William A., III and Persson, Petter ^LU (2021) In Physical Chemistry Chemical Physics 23(16). p.9921-9929

Contribution to journal › Article

Polymer-Like Self-Assembled Structures from Particles with Isotropic Interactions : Dependence upon the Range of the Attraction Haddadi, Sara ^LU ; Lu, Hongduo ^LU ; Bäcklund, Marcus ; Woodward, Clifford E. and Forsman, Jan ^LU (2021) In Langmuir 37. p.6052-6061

Contribution to journal › Article

Exploring ligand dynamics in protein crystal structures with ensemble refinement Caldararu, Octav ^LU ; Ekberg, Vilhelm ^LU ; Logan, Derek T. ^LU

; Oksanen, Esko ^LU and Ryde, Ulf ^LU

(2021) In Acta Crystallographica Section D: Structural Biology 77. p.1099-1115

Contribution to journal › Article

Modelling Biomolecular Interactions of Protein Solutions : Combining Theories and Experiments Polimeni, Marco ^LU (2021)

Thesis › Doctoral thesis (compilation)

Self-Diffusive Properties of the Intrinsically Disordered Protein Histatin 5 and the Impact of Crowding Thereon : A Combined Neutron Spectroscopy and Molecular Dynamics Simulation Study Fagerberg, Eric ^LU ; Lenton, Samuel ^LU ; Nylander, Tommy ^LU ; Seydel, Tilo and Skepö, Marie ^LU (2021) In Journal of Physical Chemistry B

Contribution to journal › Article

Orientational arrest in dense suspensions of elliptical particles under oscillatory shear flows Yousefian, Zakiyeh ^LU and Trulsson, Martin ^LU

(2021) In EPL 136(3).

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Overcharging and Free Energy Barriers for Equally Charged Surfaces Immersed in Salt Solutions Stenberg, Samuel ^LU and Forsman, Jan ^LU (2021) In Langmuir 37(49). p.14360-14368

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