Computational Chemistry | Lund University Publications

; Åkerlund, Hans-Erik ^LU ; Leech, Dónal ; Larsen, Niels Bent ; Keller, Stephan Sylvest and Gorton, Lo ^LU , et al. (2018) In ACS Applied Energy Materials 1(7). p.3313-3322

Contribution to journal › Article

Small and Large, Charged Molecules in Solution and at Interfaces Tesei, Giulio ^LU (2018)

Thesis › Doctoral thesis (compilation)

Osmotic pressure in polyelectrolyte solutions : cell-model and bulk simulations Ullner, Magnus ^LU ; Qamhieh, Khawla and Cabane, Bernard ^LU (2018) In Soft Matter 14(28). p.5832-5846

Contribution to journal › Article

Generalized van der Waals Theory of Molecular Fluids in Bulk and at Surfaces Nordholm, Sture ; Forsman, Jan ^LU ; Woodward, Clifford ; Freasier, Ben and Abbas, Zareen (2018)

Book/Report › Book

Many-body depletion forces of colloids in a polydisperse polymer dispersant in the long-chain limit Nguyen, Huy S. ; Forsman, Jan ^LU and Woodward, Clifford E. (2018) In Soft Matter 14(33).

Contribution to journal › Article

Binding free energies in the SAMPL6 octa-acid host–guest challenge calculated with MM and QM methods Caldararu, Octav ^LU ; Olsson, Martin A. ^LU ; Misini Ignjatović, Majda ^LU ; Wang, Meiting and Ryde, Ulf ^LU

(2018) In Journal of Computer-Aided Molecular Design 32(10). p.1027-1046

Contribution to journal › Article

Reaction mechanism of formate dehydrogenase studied by computational methods Dong, Geng ^LU and Ryde, Ulf ^LU

(2018) In Journal of Biological Inorganic Chemistry 23(8). p.1243-1254

Contribution to journal › Article

Uncontracted basis sets for ab initio calculations of muonic atoms and molecules Ugandi, Mihkel ; Fdez. Galván, Ignacio ; Widmark, Per Olof ^LU and Lindh, Roland ^LU (2018) In International Journal of Quantum Chemistry 118(21).

Contribution to journal › Article

Replicate or alternate? Isotropic boundary conditions and implications for Ewald summation Stenqvist, B. ^LU and Lund, M. ^LU

(2018) In EPL 123(1).

Contribution to journal › Article

Multiconfigurational short-range density-functional theory for open-shell systems Hedegård, Erik Donovan ^LU ; Toulouse, Julien and Jensen, Hans Jørgen Aagaard (2018) In Journal of Chemical Physics 148(21).

Contribution to journal › Article

A novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations Alavi, Fatemeh Sadat ; Gheidi, Mahin ; Zahedi, Mansour ; Safari, Nasser and Ryde, Ulf ^LU

(2018) In Dalton Transactions 47(25). p.8283-8291

Contribution to journal › Article

Rheology and shear jamming of frictional ellipses Trulsson, Martin ^LU

(2018) In Journal of Fluid Mechanics 849. p.718-740

Contribution to journal › Article

On the difference between additive and subtractive QM/MM calculations Cao, Lili ^LU and Ryde, Ulf ^LU

(2018) In Frontiers in Chemistry 6(APR).

Contribution to journal › Article

An overview of the transport of liquid molecules through structured polymer films, barriers and composites – Experiments correlated to structure-based simulations Gårdebjer, Sofie ^LU ; Larsson, Mikael ; Gebäck, Tobias ; Skepö, Marie ^LU and Larsson, Anette (2018) In Advances in Colloid and Interface Science 256. p.48-64

Contribution to journal › Article

Strong-coupling theory of counterions between symmetrically charged walls : From crystal to fluid phases Šamaj, Ladislav ; Trulsson, Martin ^LU

and Trizac, Emmanuel (2018) In Soft Matter 14(20). p.4040-4052

Contribution to journal › Article

Hydrodynamic trapping measures the interaction between membrane-associated molecules Junghans, Victoria ^LU ; Hladilkova, Jana ^LU ; Santos, Ana Mafalda ; Lund, Mikael ^LU

; Davis, Simon J. and Jönsson, Peter ^LU (2018) In Scientific Reports 8(1).

Contribution to journal › Article

Design, Synthesis and Computational Study of Fluorinated Quinoxaline-Oligothiophene-based Conjugated Polymers with Broad Spectral Coverage Gedefaw, Desta ; Hedström, Svante ^LU ; Xia, Yuxin ; Persson, Petter ^LU and Andersson, Mats R. (2018) In ChemPhysChem 19(24). p.3393-3400

Contribution to journal › Article

Binding of Divalent Cations to Insulin : Capillary Electrophoresis and Molecular Simulations Duboué-Dijon, Elise ; Delcroix, Pauline ; Martinez-Seara, Hector ; Hladílková, Jana ^LU ; Coufal, Pavel ; Křížek, Tomáš and Jungwirth, Pavel (2018) In Journal of Physical Chemistry B 122(21). p.5640-5648

Contribution to journal › Article

New compact density matrix averaged ANO basis sets for relativistic calculations Widmark, Per Olof ^LU ; Zobel, J. Patrick ^LU ; Vysotskiy, Victor P. ^LU ; Tsuchiya, Takashi ^LU and Veryazov, Valera ^LU

(2018) In Journal of Chemical Physics 149(19).

Contribution to journal › Article

Total Description of Intrinsic Amphiphile Aggregation : Calorimetry Study and Molecular Probing Fernandez-Alvarez, Roberto ; Medoš, Žiga ; Tošner, Zdeněk ; Zhigunov, Alexander ; Uchman, Mariusz ; Hervø-Hansen, Stefan ^LU ; Lund, Mikael ^LU

; Bešter-Rogač, Marija and Matějíček, Pavel (2018) In Langmuir 34(47). p.14448-14457

Contribution to journal › Article

Higher Flexibility of Glu-172 Explains the Unusual Stereospecificity of Glyoxalase i Jafari, Sonia ; Kazemi, Nadia ; Ryde, Ulf ^LU

and Irani, Mehdi ^LU (2018) In Inorganic Chemistry 57(9). p.4944-4958

Contribution to journal › Article

Reaction mechanism of metalloenzymes studied by theoretical methods Dong, Geng ^LU (2018)

Thesis › Doctoral thesis (compilation)

Planar screening by charge polydisperse counterions Trulsson, M. ^LU

; Trizac, E. and Šamaj, L. (2018) In Journal of Physics: Condensed Matter 30(3).

Contribution to journal › Article

Insight into the reaction mechanism of lipoyl synthase : a QM/MM study Dong, Geng ^LU ; Cao, Lili ^LU and Ryde, Ulf ^LU

(2018) In Journal of Biological Inorganic Chemistry 23(2). p.221-229

Contribution to journal › Article

Tracking the picosecond deactivation dynamics of a photoexcited iron carbene complex by time-resolved X-ray scattering Leshchev, Denis ; Harlang, Tobias C.B. ^LU ; Fredin, Lisa A. ^LU ; Khakhulin, Dmitry ; Liu, Yizhu ^LU ; Biasin, Elisa ; Laursen, Mads G. ; Newby, Gemma E. ; Haldrup, Kristoffer and Nielsen, Martin M. , et al. (2018) In Chemical Science 9(2). p.405-414

Contribution to journal › Article

Exploration of H₂ binding to the [NiFe]-hydrogenase active site with multiconfigurational density functional theory Dong, Geng ^LU ; Ryde, Ulf ^LU

; Aa Jensen, Hans Jørgen and Hedegård, Erik D. ^LU (2018) In Physical Chemistry Chemical Physics 20(2). p.794-801

Contribution to journal › Article

Quantum Refinement Does Not Support Dinuclear Copper Sites in Crystal Structures of Particulate Methane Monooxygenase Cao, Lili ^LU ; Caldararu, Octav ^LU ; Rosenzweig, Amy C. and Ryde, Ulf ^LU

(2018) In Angewandte Chemie - International Edition 57(1). p.162-166

Contribution to journal › Article

QM/MM study of the reaction mechanism of sulfite oxidase Caldararu, Octav ^LU ; Feldt, Milica ; Cioloboc, Daniela ; Van Severen, Marie Céline ^LU ; Starke, Kerstin ^LU ; Mata, Ricardo A. ; Nordlander, Ebbe ^LU and Ryde, Ulf ^LU

(2018) In Scientific Reports 8(1).

Contribution to journal › Article

On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations Henriques, João ^LU ; Arleth, Lise ; Lindorff-Larsen, Kresten and Skepö, Marie ^LU (2018) In Journal of Molecular Biology 430(16). p.2521-2539

Contribution to journal › Article

Assessing the stability of free-energy perturbation calculations by performing variations in the method Manzoni, Francesco ^LU and Ryde, Ulf ^LU

(2018) In Journal of Computer-Aided Molecular Design 32(4). p.529-536

Contribution to journal › Article

Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions Cragnell, Carolina ^LU ; Rieloff, Ellen ^LU and Skepö, Marie ^LU (2018) In Journal of Molecular Biology 430(16). p.2478-2492

Contribution to journal › Article

Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking Olsson, Martin A. ^LU ; García-Sosa, Alfonso T. and Ryde, Ulf ^LU

(2018) In Journal of Computer-Aided Molecular Design 32(1). p.211-224

Contribution to journal › Article

The effect of the relative permittivity on the tactoid formation in nanoplatelet systems. A combined computer simulation, SAXS, and osmotic pressure study Jansson, Maria ^LU ; Thuresson, Axel ^LU ; Plivelic, Tomás S. ^LU ; Forsman, Jan ^LU and Skepö, Marie ^LU (2018) In Journal of Colloid and Interface Science 513. p.575-584

Contribution to journal › Article

QM/MM free-energy perturbation and other methods to estimate ligand-binding affinities Olsson, Martin ^LU (2018)

Thesis › Doctoral thesis (compilation)

Solvent control of charge transfer excited state relaxation pathways in [Fe(2,2′-bipyridine)(CN)₄]^2- Kjær, Kasper S. ^LU ; Kunnus, Kristjan ; Harlang, Tobias C.B. ^LU ; Van Driel, Tim B. ; Ledbetter, Kathryn ; Hartsock, Robert W. ; Reinhard, Marco E. ; Koroidov, Sergey ; Li, Lin and Laursen, Mads G. , et al. (2018) In Physical Chemistry Chemical Physics 20(6). p.4238-4249

Contribution to journal › Article

A classical density functional theory for the asymmetric restricted primitive model of ionic liquids Lu, Hongduo ^LU ; Nordholm, Sture ; Woodward, Clifford E. and Forsman, Jan ^LU (2018) In Journal of Chemical Physics 148(19).

Contribution to journal › Article

Fe^II Hexa N-Heterocyclic Carbene Complex with a 528 ps Metal-To-Ligand Charge-Transfer Excited-State Lifetime Chábera, Pavel ^LU ; Kjaer, Kasper S. ^LU ; Prakash, Om ^LU ; Honarfar, Alireza ; Liu, Yizhu ^LU ; Fredin, Lisa A. ^LU ; Harlang, Tobias C.B. ^LU ; Lidin, Sven ^LU ; Uhlig, Jens ^LU and Sundström, Villy ^LU , et al. (2018) In Journal of Physical Chemistry Letters 9(3). p.459-463

Contribution to journal › Article

Aggregate Size Dependence of Amyloid Adsorption onto Charged Interfaces Tesei, Giulio ^LU ; Hellstrand, Erik ^LU ; Sanagavarapu, Kalyani ^LU ; Linse, Sara ^LU ; Sparr, Emma ^LU ; Vácha, Robert and Lund, Mikael ^LU

(2018) In Langmuir 34(4). p.1266-1273

Contribution to journal › Article

Ionic liquid interface at an electrode : Simulations of electrochemical properties using an asymmetric restricted primitive model Lu, Hongduo ^LU ; Nordholm, Sture ; Woodward, Clifford E. and Forsman, Jan ^LU (2018) In Journal of Physics: Condensed Matter 30(7).

Contribution to journal › Article

Can MM/GBSA calculations be sped up by system truncation? Misini Ignjatović, Majda ^LU ; Mikulskis, Paulius ^LU ; Söderhjelm, Pär ^LU and Ryde, Ulf ^LU

(2018) In Journal of Computational Chemistry 39(7). p.361-372

Contribution to journal › Article

A correlation-hole approach to the electric double layer with counter-ions only Palaia, Ivan ; Trulsson, Martin ^LU

; Šamaj, Ladislav and Trizac, Emmanuel (2018) In Molecular Physics 116(21-22). p.3134-3146

Contribution to journal › Article

Nonclassical Hydrophobic Effect in Micellization : Molecular Arrangement of Non-Amphiphilic Structures Uchman, Mariusz ; Abrikosov, Alexei I. ^LU ; Lepšík, Martin ; Lund, Mikael ^LU

and Matějíček, Pavel (2018) In Advanced Theory and Simulations 1(1).

Contribution to journal › Article