Computational Chemistry | Lund University Publications

Ligand-centered to metal-centered activation of a Rh(iii) photosensitizer revealed by ab initio molecular dynamics simulations Losada, Iria Bolaño ^LU and Persson, Petter ^LU (2023) In Chemical Science 14(47). p.13713-13721

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Phase transitions of ionic fluids in nanoporous electrodes Emrani, Ayeh ^LU ; Woodward, Clifford E. and Forsman, Jan ^LU (2023) In European Physical Journal E 46(10).

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Variational Pair-Density Functional Theory : Dealing with Strong Correlation at the Protein Scale Scott, Mikael ^LU ; Rodrigues, Gabriel L.S. ^LU ; Li, Xin and Delcey, Mickael G. ^LU

(2023) In Journal of Chemical Theory and Computation

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Exploring the Role of Globular Domain Locations on an Intrinsically Disordered Region of p53 : A Molecular Dynamics Investigation Bakker, Michael J. ^LU ; Sørensen, Henrik V. ^LU and Skepö, Marie ^LU (2023) In Journal of Chemical Theory and Computation

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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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Conformation- and phosphorylation-dependent electron tunnelling across self-assembled monolayers of tau peptides Ashkarran, Ali Akbar ; Hosseini, Atiyeh ^LU ; Loloee, Reza ; Perry, George ; Lee, Ki Bum ; Lund, Mikael ^LU

; Ejtehadi, Mohammad Reza and Mahmoudi, Morteza (2022) In Journal of Colloid and Interface Science 606. p.2038-2050

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Modeling of inorganic ions in aqueous solution Aspelin, Vidar ^LU (2022)

Thesis › Doctoral thesis (compilation)

Counterintuitive Electrostatics upon Metal Ion Coordination to a Receptor with Two Homotopic Binding Sites Aspelin, Vidar ^LU ; Lidskog, Anna ^LU ; Solano Arribas, Carlos ; Hervø-Hansen, Stefan ^LU ; Stenqvist, Björn ^LU ; Chudoba, Richard ^LU

; Wärnmark, Kenneth ^LU and Lund, Mikael ^LU

(2022) In Journal of the American Chemical Society 144(7). p.2921-2932

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Electro-mechanically switchable hydrocarbons based on [8]annulenes Tasić, Magdalena ^LU ; Ivković, Jakov ^LU ; Carlström, Göran ^LU

; Melcher, Michaela ^LU ; Bollella, Paolo ; Bendix, Jesper ; Gorton, Lo ^LU ; Persson, Petter ^LU ; Uhlig, Jens ^LU and Strand, Daniel ^LU (2022) In Nature Communications 13(1).

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Bone mineral : A trojan horse for bone cancers. Efficient mitochondria targeted delivery and tumor eradication with nano hydroxyapatite containing doxorubicin Liu, Yang ^LU ; Nadeem, Aftab ^LU ; Sebastian, Sujeesh ^LU

; Olsson, Martin A. ^LU ; Wai, Sun N. ; Styring, Emelie ^LU ; Engellau, Jacob ^LU ; Isaksson, Hanna ^LU

; Tägil, Magnus ^LU and Lidgren, Lars ^LU , et al. (2022) In Materials Today Bio 14.

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Combining crystallography with quantum mechanics Bergmann, Justin ^LU ; Oksanen, Esko ^LU and Ryde, Ulf ^LU

(2022) In Current Opinion in Structural Biology 72. p.18-26

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Benchmarking ANO-R basis set for multiconfigurational calculations Larsson, E D ^LU ; Zobel, J P ^LU and Veryazov, V ^LU

(2022) In Electronic Structure 4(1).

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A modified Jarzynski free-energy estimator to eliminate non-conservative forces and its application in nanoparticle-membrane interactions Hosseini, Atiyeh Najla ; Lund, Mikael ^LU

and Ejtehadi, Mohammad Reza (2022) In Physical Chemistry Chemical Physics 24(6). p.3647-3654

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Anion-cation contrast of small molecule solvation in salt solutions Hervø-Hansen, Stefan ^LU ; Heyda, Jan ; Lund, Mikael ^LU

and Matubayasi, Nobuyuki (2022) In Physical Chemistry Chemical Physics 24(5). p.3238-3249

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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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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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Design Two Novel Tetrahydroquinoline Derivatives against Anticancer Target LSD1 with 3D-QSAR Model and Molecular Simulation Xu, Yongtao ; Fan, Baoyi ; Gao, Yunlong ; Chen, Yifan ; Han, Di ; Lu, Jiarui ; Liu, Taigang ; Gao, Qinghe ; Zhang, John Zenghui and Wang, Meiting ^LU (2022) In Molecules 27(23).

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Borylation in the Second Coordination Sphere of Fe^IICyanido Complexes and Its Impact on Their Electronic Structures and Excited-State Dynamics Schmid, Lucius ; Chábera, Pavel ^LU ; Rüter, Isabelle ; Prescimone, Alessandro ; Meyer, Franc ; Yartsev, Arkady ^LU

; Persson, Petter ^LU and Wenger, Oliver S. (2022) In Inorganic Chemistry 61(40). p.15853-15863

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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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Towards a multiconfigurational description of the electronic structure in solids Larsson, Ernst Dennis ^LU (2022)

Thesis › Doctoral thesis (compilation)

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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Multiscale Modelling of Atomistic Structure of Calcium Silicate Hydrate Abrikosov, Alexei I. and Veryazov, Valera ^LU

(2022) In Solid State Phenomena 338. p.123-128

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Extending relativistic linear response theory to address solvent effects Creutzberg, Joel ^LU (2022)

Thesis › Doctoral thesis (compilation)

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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Proton Transfer Pathways in Nitrogenase with and without Dissociated S2B Jiang, Hao ^LU

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

(2022) In Angewandte Chemie (International edition) 61(39).

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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)

Polymer-Mediated Interactions and Phase Behaviour of Polymer-Particle Dispersions Haddadi, Sara ^LU (2022)

Thesis › Doctoral thesis (compilation)

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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Polarizable Embedding Complex Polarization Propagator in Four- and Two-Component Frameworks Creutzberg, Joel ^LU and Hedegård, Erik D. ^LU (2022) In Journal of Chemical Theory and Computation 18(6). p.3671-3686

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Electronic polarization effects on membrane translocation of anti-cancer drugs Najla Hosseini, Atiyeh ; Lund, Mikael ^LU

and Ejtehadi, Mohammad Reza (2022) In Physical Chemistry Chemical Physics 24(20). p.12281-12292

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Boundary-Monte Carlo Method for Neutral and Charged Confined Fluids Vo, Phuong ; Forsman, Jan ^LU and Woodward, Clifford E. (2022) In Journal of Chemical Theory and Computation 18(6). p.3766-3780

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Thermodynamically Favourable States in the Reaction of Nitrogenase without Dissociation of any Sulfide Ligand Jiang, Hao ^LU

and Ryde, Ulf ^LU

(2022) In Chemistry - A European Journal 28(14).

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Interactions between conducting surfaces in salt solutions Stenberg, Samuel ^LU ; Woodward, Clifford E. and Forsman, Jan ^LU (2022) In Soft Matter 18(8). p.1636-1643

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Can Water Act as a Nucleophile in CO Oxidation Catalysed by Mo/Cu CO-Dehydrogenase? Answers from Theory Rovaletti, Anna ; Moro, Giorgio ; Cosentino, Ugo ; Ryde, Ulf ^LU

and Greco, Claudio ^LU (2022) In ChemPhysChem 23(8).

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Computational protein crystallography : How to get the most out of your data Bergmann, Justin ^LU (2022)

Thesis › Doctoral thesis (compilation)

Interfacial behaviours of ionic fluids : Theory and simulations Stenberg, Samuel ^LU (2022)

Thesis › Doctoral thesis (compilation)

Benchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins Jafari, Sonia ; Tavares Santos, Yakini A. ; Bergmann, Justin ^LU ; Irani, Mehdi ^LU and Ryde, Ulf ^LU

(2022) In Inorganic Chemistry 61(16). p.5991-6007

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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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How general is the effect of the bulkiness of organic ligands on the basicity of metal-organic catalysts? H₂-evolving Mo oxides/sulphides as case studies Rovaletti, Anna ; Ryde, Ulf ^LU

; Moro, Giorgio ; Cosentino, Ugo and Greco, Claudio ^LU (2022) In Physical chemistry chemical physics : PCCP 24(48). p.29471-29479

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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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Computationally enhanced X-ray diffraction analysis of a gold(III) complex interacting with the human telomeric DNA G-quadruplex. Unravelling non-unique ligand positioning Cirri, Damiano ; Bazzicalupi, Carla ; Ryde, Ulf ^LU

; Bergmann, Justin ^LU ; Binacchi, Francesca ; Nocentini, Alessio ; Pratesi, Alessandro ; Gratteri, Paola and Messori, Luigi (2022) In International Journal of Biological Macromolecules 211. p.506-513

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Clustering and cross-linking of the wheat storage protein α-gliadin : A combined experimental and theoretical approach Markgren, Joel ^LU ; Rasheed, Faiza ; Hedenqvist, Mikael S. ; Skepö, Marie ^LU and Johansson, Eva (2022) In International Journal of Biological Macromolecules 211. p.592-615

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Molecular dynamics simulations of the adsorption of an intrinsically disordered protein: Force field and water model evaluation in comparison with experiments Koder Hamid, Mona ^LU ; Månsson, Linda K. ^LU ; Meklesh, Viktoriia ^LU ; Persson, Per ^LU and Skepö, Marie ^LU (2022) In Frontiers in Molecular Biosciences 9.

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Molecular dynamics simulations and solid-state nuclear magnetic resonance spectroscopy measurements of C–H bond order parameters and effective correlation times in a POPC-GM3 bilayer Fridolf, Simon ^LU ; Koder Hamid, Mona ^LU ; Svenningsson, Leo ^LU ; Skepö, Marie ^LU ; Sparr, Emma ^LU and Topgaard, Daniel ^LU (2022) In Physical Chemistry Chemical Physics 24(41). p.25588-25601

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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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Ultrafast laser spectroscopy uncovers mechanisms of light energy conversion in photosynthesis and sustainable energy materials Zigmantas, Donatas ^LU

; Polívka, Tomáš ; Persson, Petter ^LU and Sundström, Villy ^LU (2022) In Chemical Physics Reviews 3(4).

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New relativistic quantum chemical methods for understanding light-induced therapeutics Hedegård, Erik Donovan ^LU and Creutzberg, Joel ^LU (2022) In Dalton Transactions 51(42). p.16055-16064

Contribution to journal › Scientific review

From dilute to concentrated solutions of intrinsically disordered proteins: Sample preparation and data collection Lenton, Samuel ^LU ; Tully, Mark D. and Skepö, Marie ^LU (2022) In Methods in Enzymology 677. p.457-478

Chapter in Book/Report/Conference proceeding › Book chapter

Charge Interactions in a Highly Charge-Depleted Protein Hervø-Hansen, Stefan ^LU ; Højgaard, Casper ; Johansson, Kristoffer Enøe ; Wang, Yong ; Wahni, Khadija ; Young, David ; Messens, Joris ; Teilum, Kaare ^LU ; Lindorff-Larsen, Kresten and Winther, Jakob Rahr (2021) In Journal of the American Chemical Society 143(6). p.2500-2508

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