Computational Chemistry

2025

Exceptionally Strong Double-Layer Barriers Generated by Polyampholyte Salt

Ribar, D., Woodward, C. E. & Forsman, J., 2025 Apr 3, In: Journal of Physical Chemistry B. 129, 17, p. 4241-4248 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Assessing the interaction between the N-terminal region of the membrane protein magnesium transporter A and a lipid bilayer

Skog, A. E., Jones, N. C., Månsson, L. K., Morth, J. P., Vrønning Hoffmann, S., Gerelli, Y. & Skepö, M., 2025 Apr, In: Journal of Colloid and Interface Science. 683, p. 663-674 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Embedded cluster approach for accurate electronic structure calculations of ²²⁹Th :CaF₂

Nalikowski, K., Veryazov, V., Beeks, K., Schumm, T. & Krośnicki, M., 2025 Mar 15, In: Physical Review B. 111, 11, 115103.

Research output: Contribution to journal › Article › peer-review

Characterization of rapeseed protein supramolecular structures obtained by aqueous extractions

Alpiger, S. B., Smith, G. N., Pedersen, J. S., Moeller, T. L., Soerensen, H. V. & Corredig, M., 2025 Mar, In: Food Hydrocolloids. 160, 110770.

Research output: Contribution to journal › Article › peer-review

Open Access

Coherent photoproduction of light vector mesons off nuclear targets in the dipole picture

Henkels, C., de Oliveira, E. G., Pasechnik, R. & Trebien, H., 2025 Mar, In: Nuclear Physics A. 1055, 123018.

Research output: Contribution to journal › Article › peer-review

Impact of Varying Velocities and Solvation Boxes on Alchemical Free-Energy Simulations

Wang, M., Jiang, H. & Ryde, U., 2025 Jan 31, (E-pub ahead of print) In: Journal of Chemical Information and Modeling.

Research output: Contribution to journal › Article › peer-review

Open Access

The Cu_B site in particulate methane monooxygenase may be used to produce hydrogen peroxide

Lundgren, K. J. M., Cao, L., Torbjörnsson, M., Hedegård, E. D. & Ryde, U., 2025 Jan 16, In: Dalton Transactions. 54, 8, p. 3141-3156 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Lysozyme revisited

Oksanen, E., 2025 Jan, In: Structure. 33, 1, p. 6-7 2 p.

Research output: Contribution to journal › Debate/Note/Editorial › peer-review

Strong electrostatic attraction drives milk heteroprotein complex coacervation

Vinterbladh, I., Soussi, R. H., Forsman, J., Bouhallab, S. & Lund, M., 2025 Jan, In: International Journal of Biological Macromolecules. 286, 137790.

Research output: Contribution to journal › Article › peer-review

Open Access

2024

Enhanced diffusion through multivalency

Bartoš, L., Lund, M. & Vacha, R., 2024 Dec, In: Soft Matter. 21, 2, p. 179-185 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Exploring the factors influencing the ketoenamine-enolimine tautomeric equilibrium of pyridoxal 5′-phosphate in branched-chain aminotransferases

Li, X., Yu, H., Sun, J. & Sun, X., 2024 Dec, In: Molecular Catalysis. 569, 114581.

Research output: Contribution to journal › Article › peer-review

The winter holidays are glorious-except when they're not

Kamerlin, S. C. L., 2024 Dec, In: EMBO Reports. 25, 12, p. 5223-5224 2 p.

Research output: Contribution to journal › Debate/Note/Editorial

Open Access

Investigating the Substrate Oxidation Mechanism in Lytic Polysaccharide Monooxygenase: H₂O₂- versus O₂-Activation

Hagemann, M. M., Wieduwilt, E. K., Ryde, U. & Hedegård, E. D., 2024 Nov 18, In: Inorganic Chemistry. 63, 46, p. 21929-21940 12 p.

Research output: Contribution to journal › Article › peer-review

Quantum refinement in real and reciprocal space using the Phenix and ORCA software

Lundgren, K. J. M., Caldararu, O., Oksanen, E. & Ryde, U., 2024 Nov 1, In: IUCrJ. 11, Pt 6, p. 921-937 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

QM/MM Studies of Nitrogenase

Jiang, H., 2024 Sept 27, Lund: Lund University (Media-Tryck). 225 p.

Research output: Thesis › Doctoral Thesis (compilation)

File

303 Downloads (Pure)

Anisotropic coarse-grain Monte Carlo simulations of lysozyme, lactoferrin, and NISTmAb by precomputing atomistic models

Hatch, H. W., Bergonzo, C., Blanco, M. A., Yuan, G., Grudinin, S., Lund, M., Curtis, J. E., Grishaev, A. V., Liu, Y. & Shen, V. K., 2024 Sept, In: Journal of Chemical Physics. 161, 9, 094113.

Research output: Contribution to journal › Article › peer-review

Rubus wahlbergii and related species in Sweden

Zhou, M., Montes, M. S., Mattsson, T., Burén, T., Hedrén, M. & Ryde, U., 2024 Sept, In: Nordic Journal of Botany. 2024, 9, e04373.

Research output: Contribution to journal › Article › peer-review

Open Access

Cluster Formation Induced by Local Dielectric Saturation in Restricted Primitive Model Electrolytes

Ribar, D., Woodward, C. E., Nordholm, S. & Forsman, J., 2024 Aug 15, In: The Journal of Physical Chemistry Letters. 15, 32, p. 8326-8333 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Reaction Mechanism for CO Reduction by Mo-Nitrogenase Studied by QM/MM

Jiang, H. & Ryde, U., 2024 Aug 14, In: Inorganic Chemistry. 63, 34, p. 15951–15963 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Deeper Insight of the Conformational Ensemble of Intrinsically Disordered Proteins

Svensson, O., Bakker, M. J. & Skepö, M., 2024 Aug, In: Journal of Chemical Information and Modeling. 64, 15, p. 6105-6114 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Translocation of Antimicrobial Peptides across Model Membranes: The Role of Peptide Chain Length

Skog, A. E., Paracini, N., Gerelli, Y. & Skepö, M., 2024 Aug, In: Molecular Pharmaceutics. 21, 8, p. 4082-4097 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Using Iron L-Edge and Nitrogen K-Edge X-ray Absorption Spectroscopy to Improve the Understanding of the Electronic Structure of Iron Carbene Complexes

Guo, M., Temperton, R., D’Acunto, G., Johansson, N., Jones, R., Handrup, K., Ringelband, S., Prakash, O., Fan, H., de Groot, L. H. M., Hlynsson, V. F., Kaufhold, S., Gordivska, O., Velásquez González, N., Wärnmark, K., Schnadt, J., Persson, P. & Uhlig, J., 2024 Jul 8, In: Inorganic Chemistry. 63, 27, p. 12457-12468 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

CO Oxidation Mechanism of Silver-Substituted Mo/Cu CO-Dehydrogenase – Analogies and Differences to the Native Enzyme

Rovaletti, A., Moro, G., Cosentino, U., Ryde, U. & Greco, C., 2024 Jul 2, In: ChemPhysChem. 25, 13, e202400293.

Research output: Contribution to journal › Article › peer-review

Open Access

Exploring the Functional Landscape of the p53 Regulatory Domain: The Stabilizing Role of Post-Translational Modifications

Bakker, M. J., Svensson, O., So̷rensen, H. V. & Skepö, M., 2024 Jul, In: Journal of Chemical Theory and Computation. 20, 14, p. 5842-5853 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Strong-coupling effective-field theory for asymmetrically charged plates with counterions only

Šamaj, L., Trizac, E. & Trulsson, M., 2024 Jul, In: Physical Review E. 110, 1, 014609.

Research output: Contribution to journal › Article › peer-review

Putative reaction mechanism of nitrogenase with a half-dissociated S2B ligand

Jiang, H. & Ryde, U., 2024 Jun 20, In: Dalton Transactions. 53, 27, p. 11500-11513 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Perspective: multi-configurational methods in bio-inorganic chemistry

Jørgensen, F. K., Delcey, M. G. & Hedegård, E. D., 2024 Jun 7, In: Physical Chemistry Chemical Physics. 26, 25, p. 17443-17455 13 p.

Research output: Contribution to journal › Review article › peer-review

Unraveling the Binding Mode of Cyclic Adenosine–Inosine Monophosphate (cAIMP) to STING through Molecular Dynamics Simulations

Wang, M., Fan, B., Lu, W., Ryde, U., Chang, Y., Han, D., Lu, J., Liu, T., Gao, Q., Chen, C. & Xu, Y., 2024 Jun, In: Molecules. 29, 11, 2650.

Research output: Contribution to journal › Article › peer-review

Open Access

Side-group switching between metal-to-ligand charge-transfer and metal-centered excited state properties in iron(II) N-heterocyclic carbene complexes

Lindh, L., Rosemann, N. W., Losada, I. B., Persson, S., Goriya, Y., Fan, H., Gordivska, O., Wärnmark, K., Uhlig, J., Chábera, P., Yartsev, A. & Persson, P., 2024 May 1, In: Coordination Chemistry Reviews. 506, 215709.

Research output: Contribution to journal › Review article › peer-review

Open Access

Influence of Selective Carbon 1s Excitation on Auger–Meitner Decay in the ESCA Molecule

Fouda, A., Lindblom, V., Southworth, S. H., Doumy, G., Ho, P., Young, L., Cheng, L. & Sorensen, S. L., 2024 Apr 24, In: Journal of Physical Chemistry Letters. 15, 16, p. 4286-4293 8.

Research output: Contribution to journal › Article › peer-review

Open Access

Interplay of halogen bonding and solvation in protein-ligand binding

Verteramo, M. L., Ignjatović, M. M., Kumar, R., Wernersson, S., Ekberg, V., Wallerstein, J., Carlström, G., Chadimová, V., Leffler, H., Zetterberg, F., Logan, D. T., Ryde, U., Akke, M. & Nilsson, U. J., 2024 Apr 19, In: iScience. 27, 4, 109636.

Research output: Contribution to journal › Article › peer-review

Open Access

A comprehensive exploration of structural and electronic properties of molybdenum clusters

Wei, Y., Veryazov, V. & Kantorovich, L., 2024 Mar 1, In: APL Materials. 12, 3, 031127.

Research output: Contribution to journal › Article › peer-review

Open Access

A multi-scale numerical approach to study monoclonal antibodies in solution

Polimeni, M., Zaccarelli, E., Gulotta, A., Lund, M., Stradner, A. & Schurtenberger, P., 2024 Mar 1, In: APL Bioengineering. 8, 1, 016111.

Research output: Contribution to journal › Article › peer-review

Open Access

How Rigidity and Conjugation of Bidentate Ligands Affect the Geometry and Photophysics of Iron N-Heterocyclic Complexes: A Comparative Study

Prakash, O., Chábera, P., Kaul, N., Hlynsson, V. F., Rosemann, N. W., Losada, I. B., Hoang Hai, Y. T., Huang, P., Bendix, J., Ericsson, T., Häggström, L., Gupta, A. K., Strand, D., Yartsev, A., Lomoth, R., Persson, P. & Wärnmark, K., 2024 Mar, In: Inorganic Chemistry. 63, 10, p. 4461-4473 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Modeling Photofunctional Transition Metal Complexes

Bolano Losada, I., 2024 Mar, Lund, Sweden: Division of Theoretical Chemistry, Department of Chemistry, Lund University. 250 p.

Research output: Thesis › Doctoral Thesis (compilation)

Open Access

File

216 Downloads (Pure)

QM/MM study of the catalytic reaction of aphid myrosinase

Jafari, S., Ryde, U. & Irani, M., 2024 Mar, In: International Journal of Biological Macromolecules. 262, 130089.

Research output: Contribution to journal › Article › peer-review

Open Access

File

1 Downloads (Pure)

Hydrogen bonding in glassy trehalose-water system: Insights from density functional theory and molecular dynamics simulations

Kocherbitov, V., Music, D. & Veryazov, V., 2024 Feb 28, In: Journal of Chemical Physics. 160, 8, 084504.

Research output: Contribution to journal › Article › peer-review

Open Access

Scalar Relativistic All-Electron and Pseudopotential Ab Initio Study of a Minimal Nitrogenase [Fe(SH)₄H]⁻ Model Employing Coupled-Cluster and Auxiliary-Field Quantum Monte Carlo Many-Body Methods

Vysotskiy, V. P., Filippi, C. & Ryde, U., 2024 Feb 22, In: Journal of Physical Chemistry A. 128, 7, p. 1358-1374 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Photoredox matching of earth-abundant photosensitizers with hydrogen evolving catalysts by first-principles predictions

Losada, I. B. & Persson, P., 2024 Feb, In: Journal of Chemical Physics. 160, 7, 074302.

Research output: Contribution to journal › Article › peer-review

Open Access

Tailoring the Photophysical Properties of a Homoleptic Iron(II) Tetra N-Heterocyclic Carbene Complex by Attaching an Imidazolium Group to the (C^∧N^∧C) Pincer Ligand─A Comparative Study

Prakash, O., Lindh, L., Gupta, A. K., Hoang Hai, Y. T., Kaul, N., Chábera, P., Lindgren, F., Ericsson, T., Häggström, L., Strand, D., Yartsev, A., Lomoth, R., Persson, P. & Wärnmark, K., 2024 Feb, In: Inorganic Chemistry. 63, 6, p. 2909-2918 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Variational Pair-Density Functional Theory: Dealing with Strong Correlation at the Protein Scale

Scott, M., Rodrigues, G. L. S., Li, X. & Delcey, M. G., 2024 Jan 13, In: Journal of Chemical Theory and Computation. 20, 6

Research output: Contribution to journal › Article › peer-review

Open Access

Time-resolved scattering methods for biological samples at the CoSAXS beamline, MAX IV Laboratory

Herranz-Trillo, F., Sørensen, H. V., Dicko, C., Pérez, J., Lenton, S., Foderà, V., Fornell, A., Skepö, M., Plivelic, T. S., Berntsson, O., Andersson, M., Magkakis, K., Orädd, F., Ahn, B., Appio, R., Da Silva, J., Da Silva, V., Lerato, M. & Terry, A. E., 2024 Jan, Time-Resolved Methods in Structural Biology. Academic Press, p. 245-296 52 p. (Methods in Enzymology; vol. 709).

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

An efficient method to establish electrostatic screening lengths of restricted primitive model electrolytes

Forsman, J., Ribar, D. & Woodward, C. E., 2024, In: Physical Chemistry Chemical Physics. 26, 29, p. 19921-19933 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Convergence criteria for single-step free-energy calculations: the relation between the Π bias measure and the sample variance

Wang, M., Mei, Y. & Ryde, U., 2024, In: Chemical Science. 15, 23, p. 8786-8799 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Exploring the Role of Globular Domain Locations on an Intrinsically Disordered Region of p53: A Molecular Dynamics Investigation

Bakker, M. J., Sørensen, H. V. & Skepö, M., 2024, In: Journal of Chemical Theory and Computation. 20, 3, p. 1423–1433 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

H₂ formation from the E₂–E₄ states of nitrogenase

Jiang, H. & Ryde, U., 2024, In: Physical Chemistry Chemical Physics. 26, 2, p. 1364-1375 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Interactions of intrinsically disordered peptides with phospholipid bilayers

Eriksson Skog, A., 2024, Lund University. 241 p.

Research output: Thesis › Doctoral Thesis (compilation)

File

66 Downloads (Pure)

Lipid shape and packing are key for optimal design of pH-sensitive mRNA lipid nanoparticles

Tesei, G., Hsiao, Y. W., Dabkowska, A., Grõnberg, G., Arteta, M. Y., Ulkoski, D., Bray, D. J., Trulsson, M., Ulander, J., Lund, M. & Lindfors, L., 2024, In: Proceedings of the National Academy of Sciences of the United States of America. 121, 2, e2311700120.

Research output: Contribution to journal › Article › peer-review

Open Access

2023

A numerical study on orientational arrest and size segregation of dense particle flows using discrete element modeling

Yousefian, Z., 2023 Dec 19, Lund: Lund University (Media-Tryck).

Research output: Thesis › Licentiate Thesis

Open Access

File

7 Downloads (Pure)

Multifaceted Deactivation Dynamics of Fe(II) N-Heterocyclic Carbene Photosensitizers

Lindh, L., Pascher, T., Persson, S., Goriya, Y., Wärnmark, K., Uhlig, J., Chábera, P., Persson, P. & Yartsev, A., 2023 Dec, In: Journal of Physical Chemistry A. 127, 48, p. 10210-10222 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Computational Chemistry

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