SwePub
Sök i SwePub databas

  Utökad sökning

Träfflista för sökning "L773:1549 9618 OR L773:1549 9626 "

Sökning: L773:1549 9618 OR L773:1549 9626

  • Resultat 1-50 av 287
Sortera/gruppera träfflistan
   
NumreringReferensOmslagsbildHitta
1.
  • Allnér, Olof, et al. (författare)
  • Magnesium ion–water coordination and exchange in biomolecular simulations
  • 2012
  • Ingår i: Journal of Chemical Theory and Computation. - Stockholm : Karolinska Institutet, Dept of Biosciences and Nutrition. - 1549-9618 .- 1549-9626.
  • Tidskriftsartikel (refereegranskat)abstract
    • Magnesium ions have an important role in the structure and folding mechanism of ribonucleic systems. To properly simulate these biophysical processes, the applied molecular models should reproduce, among others, the kinetic properties of the ions in water solution. Here, we have studied the kinetics of the binding of magnesium ions with water molecules and nucleic acids systems using molecular dynamics simulation in detail. We have validated the parameters used in biomolecular force fields, such as AMBER and CHARMM, for Mg2+ ions, and also for the biological relevant ions, Na+, K+ and Ca2+ together with three different water models (TIP3P, SPC/E and TIP5P). The results show that Mg2+ ions have a slower exchange rate than Na+, K+ and Ca2+ in agreement with experimental trend, but the simulated value underestimates the experimentally observed Mg2+-water exchange rate with several orders of magnitudes, irrespective of force field and water model. A new set of parameters for Mg2+ was developed to reproduce the experimental kinetic data. This set also leads to better reproduction of structural data than existing models. We have applied the new parameters set to Mg2+ binding with a mono-phosphate model system and with the purine riboswitch, add A-riboswitch. In line with the Mg2+-water results, the newly developed parameters show a better description of the structure and kinetic of the Mg2+-phosphate binding than all other models. The characterization of the ion binding to the riboswitch system shows that the new parameter set does not affect the global structure of the ribonucleic acid system or the number of ions involved in direct or indirect binding. A slight decrease in the number of water-bridged contacts between A-riboswitch and Mg2+ ion is observed. The results support the ability of the newly developed parameters to improve the kinetic description of the Mg2+ and phosphate ions and their applicability in nucleic acid simulation.
  •  
2.
  • Abraham, Mark J, et al. (författare)
  • Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations
  • 2008
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 4:7
  • Tidskriftsartikel (refereegranskat)abstract
    • We address the question of constructing a protocol for replica-exchange molecular dynamics (REMD) simulations that make efficient use of the replica space, assess whether published applications are achieving such "mixing" efficiency, and provide a how-to guide to assist users to plan efficient REMD simulations. To address our first question, we introduce and discuss three metrics for assessing the number of replica-exchange attempts required to justify the use of a replica scheme and define a "transit number" as the lower bound for the length of an efficient simulation. Our literature survey of applications of REMD simulations of peptides in explicit solvent indicated that authors are not routinely reporting sufficient details of their simulation protocols to allow readers to make independent assessments of the impact of the method on their results, particularly whether mixing efficiency has been achieved. Necessary details include the expected or observed replica-exchange probability, together with the total number of exchange attempts, the exchange period, and estimates of the autocorrelation time of the potential energy. Our analysis of cases where the necessary information was reported suggests that in many of these simulations there are insufficient exchanges attempted or an insufficiently long period between them to provide confidence that the simulation length justifies the size of the replica scheme. We suggest guidelines for designing REMD simulation protocols to ensure mixing efficiency. Two key recommendations are that the exchange period should in general be larger than 1 ps and the number of exchange attempts should be chosen to significantly exceed the transit number for the replica scheme.
  •  
3.
  • Aho, Noora, et al. (författare)
  • Scalable Constant pH Molecular Dynamics in GROMACS
  • 2022
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 18:10, s. 6148-6160
  • Tidskriftsartikel (refereegranskat)abstract
    • Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414–2423] was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to the poor scaling of that code with respect to the number of titratable sites. To overcome this limitation, we implemented an alternative scheme for interpolating the Hamiltonians of the protonation states that makes the constant pH molecular dynamics simulations almost as fast as a normal MD simulation with GROMACS. In addition, we implemented a simpler scheme, called multisite representation, for modeling side chains with multiple titratable sites, such as imidazole rings. This scheme, which is based on constraining the sum of the λ-coordinates, not only reduces the complexity associated with parametrizing the intramolecular interactions between the sites but also is easily extendable to other molecules with multiple titratable sites. With the combination of a more efficient interpolation scheme and multisite representation of titratable groups, we anticipate a rapid uptake of constant pH molecular dynamics simulations within the GROMACS user community.
  •  
4.
  • Ali, Md Ehesan, et al. (författare)
  • Designing the Redox-Driven Switching of Ferro- to Antiferromagnetic Couplings in Organic Diradicals
  • 2013
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 9:12, s. 5216-5220
  • Tidskriftsartikel (refereegranskat)abstract
    • Switching of the magnetic exchange coupling from ferro- to antiferromagnetic or vice versa in a single molecule is an appealing but rarely occurring phenomenon in molecular magnetism. Here, we report this for an unprecedented pure organic system, computationally designed by tailoring a conformationally restricted, known nitroxide-diradical (Rajca et al. J. Am. Chem. Soc. 2007, 129, 10159). This ferro- to antiferromagnetic coupling switching of an "m-phenylene" based diradical is governed by a stereoelectronic effect and controlled by a redox-driven chemical reaction.
  •  
5.
  • Almlöf, Martin, et al. (författare)
  • Improving the accuracy of the linear interaction energy method for solvation free energies
  • 2007
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 3:6, s. 2162-2175
  • Tidskriftsartikel (refereegranskat)abstract
    • A linear response method for estimating the free energy of solvation is presented and validated using explicit solvent molecular dynamics, thermodynamic perturbation calculations, and experimental data. The electrostatic contribution to the solvation free energy is calculated using a linear response estimate, which is obtained by comparison to the free energy calculated using thermodynamic perturbation. Systematic deviations from the value of 1/2 in the potential energy scaling factor are observed for some types of compounds, and these are taken into account by introducing specific coefficients for different chemical groups. The derived model reduces the rms error of the linear response estimate significantly from 1.6 to 0.3 kcal/mol on a training set of 221 molecules used to parametrize the model and from 3.7 to 1.3 kcal/mol on a test set of 355 molecules that were not used in the derivation of the model. The total solvation free energy is estimated by combining the derived model with an empirical size dependent term for predicting the nonpolar contribution. Using this model, the experimental hydration free energies for 192 molecules are reproduced with an rms error of 1.1 kcal/mol. The use of LIE in simplified binding free energy calculations to predict protein−ligand binding free energies is also discussed.
  •  
6.
  • Ammothum Kandy, Akshay Krishna, et al. (författare)
  • Curvature Constrained Splines for DFTB Repulsive Potential Parametrization
  • 2021
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 17:3, s. 1771-1781
  • Tidskriftsartikel (refereegranskat)abstract
    • The Curvature Constrained Splines (CCS) methodology has been used for fitting repulsive potentials to be used in SCC-DFTB calculations. The benefit of using CCS is that the actual fitting of the repulsive potential is performed through quadratic programming on a convex objective function. This guarantees a unique (for strictly convex) and optimum two-body repulsive potential in a single shot, thereby making the parametrization process robust, and with minimal human effort. Furthermore, the constraints in CCS give the user control to tune the shape of the repulsive potential based on prior knowledge about the system in question. Herein, we developed the method further with new constraints and the capability to handle sparse data. We used the method to generate accurate repulsive potentials for bulk Si polymorphs and demonstrate that for a given Slater-Koster table, which reproduces the experimental band structure for bulk Si in its ground state, we are unable to find one single two-body repulsive potential that can accurately describe the various bulk polymorphs of silicon in our training set. We further demonstrate that to increase transferability, the repulsive potential needs to be adjusted to account for changes in the chemical environment, here expressed in the form of a coordination number. By training a near-sighted Atomistic Neural Network potential, which includes many-body effects but still essentially within the first-neighbor shell, we can obtain full transferability for SCC-DFTB in terms of describing the energetics of different Si polymorphs.
  •  
7.
  • Aquilante, Francesco, et al. (författare)
  • Cholesky decomposition-based multiconfiguration second-order perturbation theory (CD-CASPT2) : application to the spin-state energetics of Co-III(diiminato)(NPh).
  • 2008
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 4:5, s. 694-702
  • Tidskriftsartikel (refereegranskat)abstract
    • The electronic structure and low-lying electronic states of a Co-III(diiminato)(NPh) complex have been studied using mulficonfigurational wave function theory (CASSCF/CASPT2) The results have been compared to those obtained with density functional theory. The best agreement with ab initio results is obtained with a modified B3LYP functional containing a reduced amount (15%) of Hartree-Fock exchange. A relativistic basis set with 869 functions has been employed in the most extensive ab initio calculations, where a Cholesky decomposition technique was used to overcome problems arising from the large size of the two-electron integral matrix. It is shown that this approximation reproduces results obtained with the full integral set to a high accuracy, thus opening the possibility to use this approach to perform multiconfigurational wave-function-based quantum chemistry on much larger systems relative to what has been possible until now.
  •  
8.
  • Badri, Zahra, et al. (författare)
  • All-Metal Aromaticity : Revisiting the Ring Current Model among Transition Metal Clusters
  • 2013
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 9:11, s. 4789-4796
  • Tidskriftsartikel (refereegranskat)abstract
    • We present new insight into the nature of aromaticity in metal clusters. We give computational arguments in favor of using the ring-current model over local indices, such as nucleus independent chemical shifts, for the determination of the magnetic aromaticity. Two approaches for estimating magnetically induced ring currents are employed for this purpose, one based on the quantum theory of atoms in molecules (QTAIM) and the other where magnetically induced current densities (MICD) are explicitly calculated. We show that the two-zone aromaticity/antiaromaticity of a number of 3d metallic clusters (Sc-3(-), Cu-3(+), and Cu-4(2-)) can be explained using the QTAIM-based magnetizabilities. The reliability of the calculated atomic and bond magnetizabilities of the metallic clusters are verified by comparison with MICD computed at the multiconfiguration self-consistent field (MCSCF) and density functional levels of theory. Integrated MCSCF current strength susceptibilities as well as a visual analysis of the calculated current densities confirm the interpretations based on the QTAIM magnetizabilities. In view of the new findings, we suggest a simple explanation based on classical electromagnetic theory to explain the anomalous magnetic shielding in different transition metal clusters. Our results suggest that the nature of magnetic aromaticity/antiaromaticity in transition-metal clusters should be assessed more carefully based on global indices.
  •  
9.
  • Barcza, Gergely, et al. (författare)
  • DMRG on Top of Plane-Wave Kohn-Sham Orbitals: A Case Study of Defected Boron Nitride
  • 2021
  • Ingår i: Journal of Chemical Theory and Computation. - : AMER CHEMICAL SOC. - 1549-9618 .- 1549-9626. ; 17:2, s. 1143-1154
  • Tidskriftsartikel (refereegranskat)abstract
    • In this paper, we analyze the numerical aspects of the inherent multireference density matrix renormalization group (DMRG) calculations on top of the periodic Kohn-Sham density functional theory using the complete active space approach. The potential of the framework is illustrated by studying hexagonal boron nitride nanoflakes embedding a charged single boron vacancy point defect by revealing a vertical energy spectrum with a prominent multireference character. We investigate the consistency of the DMRG energy spectrum from the perspective of sample size, basis size, and active space selection protocol. Results obtained from standard quantum chemical atom-centered basis calculations and plane-wave based counterparts show excellent agreement. Furthermore, we also discuss the spectrum of the periodic sheet which is in good agreement with extrapolated data of finite clusters. These results pave the way toward applying the DMRG method in extended correlated solid-state systems, such as point defect qubit in wide band gap semiconductors.
  •  
10.
  • Barucha-Dobrautz, Werner, 1987, et al. (författare)
  • Toward Real Chemical Accuracy on Current Quantum Hardware Through the Transcorrelated Method
  • 2024
  • Ingår i: Journal of Chemical Theory and Computation. - 1549-9626 .- 1549-9618. ; 20:10, s. 4146-4160
  • Tidskriftsartikel (refereegranskat)abstract
    • Quantum computing is emerging as a new computational paradigm with the potential to transform several research fields including quantum chemistry. However, current hardware limitations (including limited coherence times, gate infidelities, and connectivity) hamper the implementation of most quantum algorithms and call for more noise-resilient solutions. We propose an explicitly correlated Ansatz based on the transcorrelated (TC) approach to target these major roadblocks directly. This method transfers, without any approximation, correlations from the wave function directly into the Hamiltonian, thus reducing the resources needed to achieve accurate results with noisy quantum devices. We show that the TC approach allows for shallower circuits and improves the convergence toward the complete basis set limit, providing energies within chemical accuracy to experiment with smaller basis sets and, thus, fewer qubits. We demonstrate our method by computing bond lengths, dissociation energies, and vibrational frequencies close to experimental results for the hydrogen dimer and lithium hydride using two and four qubits, respectively. To demonstrate our approach’s current and near-term potential, we perform hardware experiments, where our results confirm that the TC method paves the way toward accurate quantum chemistry calculations already on today’s quantum hardware.
  •  
11.
  • Battaglia, Stefano, et al. (författare)
  • Extended Dynamically Weighted CASPT2 : The Best of Two Worlds
  • 2020
  • Ingår i: Journal of Chemical Theory and Computation. - : AMER CHEMICAL SOC. - 1549-9618 .- 1549-9626. ; 16:3, s. 1555-1567
  • Tidskriftsartikel (refereegranskat)abstract
    • We introduce a new variant of the complete active A space second-order perturbation theory (CASPT2) method that performs similarly to multistate CASPT2 (MS-CASPT2) in regions of the potential energy surface where the electronic states are energetically well separated and is akin to extended MS-CASPT2 (XMS-CASPT2) in case the underlying zeroth-order references are near-degenerate. Our approach follows a recipe analogous to that of XMS-CASPT2 to ensure approximate invariance under unitary transformations of the model states and a dynamic weighting scheme to smoothly interpolate the Fock operator between state-specific and state-average regimes. The resulting extended dynamically weighted CASPT2 (XDW-CASPT2) methodology possesses the most desirable features of both MS-CASPT2 and XMS-CASPT2, that is, the ability to provide accurate transition energies and correctly describe avoided crossings and conical intersections. The reliability of XDW-CASPT2 is assessed on a number of molecular systems. First, we consider the dissociation of lithium fluoride, highlighting the distinctive characteristics of the new approach. Second, the invariance of the theory is investigated by studying the conical intersection of the distorted allene molecule. Finally, the relative accuracy in the calculation of vertical excitation energies is benchmarked on a set of 26 organic compounds. We found that XDW-CASPT2, albeit being only approximately invariant, produces smooth potential energy surfaces around conical intersections and avoided crossings, performing equally well to the strictly invariant XMS-CASPT2 method. The accuracy of vertical transition energies is almost identical to MS-CASPT2, with a mean absolute deviation of 0.01-0.02 eV, in contrast to 0.12 eV for XMS-CASPT2.
  •  
12.
  • Battaglia, Stefano, et al. (författare)
  • Regularized CASPT2 : an Intruder-State-Free Approach
  • 2022
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 18:8, s. 4814-4825
  • Tidskriftsartikel (refereegranskat)abstract
    • In this work we present a new approach to fix the intruder-state problem (ISP) in CASPT2 based on sigma p regularization. The resulting sigma(p)-CASPT2 method is compared to previous techniques, namely, the real and imaginary level shifts, on a theoretical basis and by performing a series of systematic calculations. The analysis is focused on two aspects, the effectiveness of sigma(p)-CASPT2 in removing the ISP and the sensitivity of the approach with respect to the input parameter. We found that sigma p- CASPT2 compares favorably with respect to previous approaches and that different versions, sigma(1)-CASPT2 and sigma(2)-CASPT2, have different potential application domains. This analysis also reveals the unsuitability of the real level shift technique as a general way to avoid the intruder-state problem.
  •  
13.
  • Bil, Andrzej, et al. (författare)
  • Photoinduced Double Proton Transfer in the Glyoxal-Methanol Complex Revisited: The Role of the Excited States
  • 2020
  • Ingår i: Journal of Chemical Theory and Computation. - : AMER CHEMICAL SOC. - 1549-9618 .- 1549-9626. ; 16:5, s. 3273-3286
  • Tidskriftsartikel (refereegranskat)abstract
    • Under irradiation in the visible range, the glyoxal-methanol complex in a cryogenic argon matrix undergoes a double proton transfer (DPT) reaction through which the glyoxal molecule isomerizes into hydroxyketene. In this work, we employ electronic structure simulations in order to shed more light on the underlying mechanism. Rewardingly, we find that the lowest singlet excited state (S-1) of the complex acts as a gateway to two previously unknown isomerization pathways, of which one takes place entirely in the singlet manifold and the other also involves the lowest triplet state (T-1). Both of these pathways are fully compatible with the available experimental data, implying that either or both are operative under experimental conditions. In either pathway, the methanol molecule acts as a proton shuttle between the proton-donating and proton-accepting sites of glyoxal, resulting in a dramatic lowering of the potential energy barrier to isomerization with respect to the case of isolated glyoxal. The occurrence of DPT in the singlet manifold is demonstrated directly with the use of nonadiabatic molecular dynamics simulations at the spin-flip time-dependent density functional theory level.
  •  
14.
  • Bjelkmar, Pär, 1980-, et al. (författare)
  • Implementation of the CHARMM Force Field in GROMACS : Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models
  • 2010
  • Ingår i: Journal of Chemical Theory and Computation. - Washington : American Chemical Society. - 1549-9618 .- 1549-9626. ; 6:2, s. 459-466
  • Tidskriftsartikel (refereegranskat)abstract
    • CHARMM27 is a widespread and popular force field for biomolecular simulation, and several recent algorithms such as implicit solvent models have been developed specifically for it. We have here implemented the CHARMM force field and all necessary extended functional forms in the GROMACS molecular simulation package, to make CHARMM-specific features available and to test them in combination with techniques for extended time steps, to make all major force fields available for comparison studies in GROMACS, and to test various solvent model optimizations, in particular the effect of Lennard-Jones interactions on hydrogens. The implementation has full support both for CHARMM-specific features such as multiple potentials over the same dihedral angle and the grid-based energy correction map on the , ψ protein backbone dihedrals, as well as all GROMACS features such as virtual hydrogen interaction sites that enable 5 fs time steps. The medium-to-long time effects of both the correction maps and virtual sites have been tested by performing a series of 100 ns simulations using different models for water representation, including comparisons between CHARMM and traditional TIP3P. Including the correction maps improves sampling of near native-state conformations in our systems, and to some extent it is even able to refine distorted protein conformations. Finally, we show that this accuracy is largely maintained with a new implicit solvent implementation that works with virtual interaction sites, which enables performance in excess of 250 ns/day for a 900-atom protein on a quad-core desktop computer.
  •  
15.
  • Björling, Alexander, 1983, et al. (författare)
  • Deciphering solution scattering data with experimentally guided molecular dynamics simulations
  • 2015
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 11:2, s. 780-787
  • Tidskriftsartikel (refereegranskat)abstract
    • Time-resolved X-ray solution scattering is an increasingly popular method to measure conformational changes in proteins. Extracting structural information from the resulting difference X-ray scattering data is a daunting task. We present a method in which the limited but precious information encoded in such scattering curves is combined with the chemical knowledge of molecular force fields. The molecule of interest is then refined toward experimental data using molecular dynamics simulation. Therefore, the energy landscape is biased toward conformations that agree with experimental data. We describe and verify the method, and we provide an implementation in GROMACS.
  •  
16.
  • Bokareva, O. S., et al. (författare)
  • Optimized long-range corrected density functionals for electronic and optical properties of bare and ligated CdSe quantum dots
  • 2017
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 13:1, s. 110-116
  • Tidskriftsartikel (refereegranskat)abstract
    • The reliable prediction of optical and fundamental gaps of finite size systems using density functional theory requires to account for the potential self-interaction error, which is notorious for degrading the description of charge transfer transitions. One solution is provided by parametrized long-range corrected functionals such as LC-BLYP, which can be tuned such as to describe certain properties of the particular system at hand. Here, bare and 3-mercaptoprotionic acid covered Cd33Se33 quantum dots are investigated using the optimally tuned LC-BLYP functional. The range separation parameter, which determines the switching on of the exact exchange contribution, is found to be 0.12 bohr-1 and 0.09 bohr-1 for the bare and covered quantum dot, respectively. It is shown that density functional optimization indeed yields optical and fundamental gaps and thus exciton binding energies, considerably different compared with standard functionals such as the popular PBE and B3LYP ones. This holds true, despite the well established fact that the leading transitions are localized on the quantum dot and do not show pronounced long-range charge transfer character.
  •  
17.
  • Borstnar, Rok, et al. (författare)
  • Computational Study of the pK(a) Values of Potential Catalytic Residues in the Active Site of Monoamine Oxidase B
  • 2012
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:10, s. 3864-3870
  • Tidskriftsartikel (refereegranskat)abstract
    • Monoamine oxidase (MAO), which exists in two isozymic forms, MAO A and MAO B, is an important flavoenzyme responsible for the metabolism of amine neurotransmitters such as dopamine, serotonin, and norepinephrine. Despite extensive research effort, neither the catalytic nor the inhibition mechanisms of MAO have been completely understood. There has also been dispute with regard to the protonation state of the substrate upon entering the active site, as well as the identity of residues that are important for the initial deprotonation of irreversible acetylenic inhibitors, in accordance with the recently proposed mechanism. Therefore, in order to investigate features essential for the modes of action of MAO, we have calculated pK(a) values of three relevant tyrosine residues in the MAO B active site, with and without dopamine bound as the. substrate (as well as the pK(a) of the dopamine itself in the active site). The calculated pK(a) values for Tyr188, Tyr398, and Tyr435 in the complex are found to be shifted upward to 13.0, 13.7, and 14.7, respectively, relative to 10.1 in aqueous solution, ruling out the likelihood that they are viable proton acceptors. The altered tyrosine pK(a) values could be rationalized as an interplay of two opposing effects: insertion of positively charged bulky dopamine that lowers tyrosine pK(a) values, and subsequent removal of water molecules from the active site that elevates tyrosine pK(a) values, in which the latter prevails. Additionally, the pK(a) value of the bound dopamine (8.8) is practically unchanged compared to the corresponding value in aqueous solution (8.9), as would be expected from a charged amine placed in a hydrophobic active site consisting of aromatic moieties. We also observed potentially favorable cation-pi interactions between the -NH3+ group on dopamine and aromatic moieties, which provide a stabilizing effect to the charged fragment. Thus, we offer here theoretical evidence that the amine is most likely to be present in the active site in its protonated form, which is similar to the conclusion from experimental studies of MAO A (Jones et al. J. Neural Trans. 2007, 114, 707-712). However, the free energy cost of transferring the proton from the substrate to the bulk solvent is only 1.9 kcal mol(-1), leaving open the possibility that the amine enters the chemical step in its neutral form. In conjunction with additional experimental and computational work, the data presented here should lead toward a deeper understanding of mechanisms of the catalytic activity and irreversible inhibition of MAO B, which can allow for the design of novel and improved MAO B inhibitors.
  •  
18.
  • Boström, Jonas, et al. (författare)
  • Ab Initio Density Fitting : Accuracy Assessment of Auxiliary Basis Sets from Cholesky Decompositions
  • 2009
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 5:6, s. 1545-1553
  • Tidskriftsartikel (refereegranskat)abstract
    • The accuracy of auxiliary basis sets derived by Cholesky decompositions of the electron repulsion integrals is assessed in a series of benchmarks on total ground state energies and dipole moments of a large test set of molecules. The test set includes molecules composed of atoms from the first three rows of the periodic table as well as transition metals. The accuracy of the auxiliary basis sets are tested for the 6-31 G**, correlation consistent, and atomic natural orbital basis sets at the Hartree-Fock, density functional theory, and second-order Moller-Plesset levels of theory. By decreasing the decomposition threshold, a hierarchy of auxiliary basis sets is obtained with accuracies ranging from that of standard auxiliary basis sets to that of conventional integral treatments.
  •  
19.
  • Boström, Jonas, et al. (författare)
  • Analytical gradients of Hartree-Fock exchange with density fitting approximations
  • 2013
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 9:1, s. 204-212
  • Tidskriftsartikel (refereegranskat)abstract
    • We extend the local exchange (LK) algorithm [Aquilante, F.; Pedersen, T. B.; Lindh, R. J. Chem. Phys.2007, 126, 194106] to the calculation of analytical gradients with density fitting. We discuss the features of the screening procedure and demonstrate the possible advantages of using this formulation, which is easily interfaced to a standard integral-direct gradient code. With auxiliary basis sets obtained from Cholesky decomposition of atomic or molecular integral blocks with a decomposition threshold of 10-4Eh, typical errors due to the density fitting in bond lengths, bond angles, and dihedral angles are 0.1 pm, 0.1°, and 0.5°, respectively. The overall speedup of geometry optimizations is about 1 order of magnitude for atomic natural-orbital-type basis sets but much less pronounced for correlation-consistent basis sets.
  •  
20.
  • Boström, Jonas, et al. (författare)
  • Calibration of Cholesky Auxiliary Basis Sets for Multiconfigurational Perturbation Theory Calculations of Excitation Energies
  • 2010
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 6:3, s. 747-754
  • Tidskriftsartikel (refereegranskat)abstract
    • The accuracy of auxiliary basis sets derived from Cholesky decomposition of two-electron integrals is assessed for excitation energies calculated at the state-average complete active space self-consistent field (CASSCF) and multiconfigurational second order perturbation theory (CASPT2) levels of theory using segmented as well as generally contracted atomic orbital basis sets. Based on 196 valence excitations in 26 organic molecules and 72 Rydberg excitations in 3 organic molecules, the results show that Cholesky auxiliary basis sets can be used without compromising the accuracy of the multiconfigurational methods. Specifically, with a decomposition threshold of 10(-4) au, the mean error due to the Cholesky auxiliary basis set is 0.001 eV, or smaller, decreasing with increasing atomic orbital basis set quality.
  •  
21.
  • Boström, Jonas, et al. (författare)
  • Coupled Cluster and Moller-Plesset Perturbation Theory Calculations of Noncovalent Intermolecular Interactions using Density Fitting with Auxiliary Basis Sets from Cholesky Decompositions
  • 2012
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:6, s. 1921-1928
  • Tidskriftsartikel (refereegranskat)abstract
    • We compute noncovalent intermolecular interaction energies for the S22 test set [Phys. Chem. Chem. Phys. 2006, 8, 1985-1993] of molecules at the Moller-Plesset and coupled cluster levels of supermolecular theory using density fitting (DF) to approximate all two-electron integrals. The error due to the DF approximation is analyzed for a range of auxiliary basis sets derived from Cholesky decomposition (CD) in conjunction with correlation consistent and atomic natural orbital valence basis sets. A Cholesky decomposition threshold of 10(-4)E(h) for full molecular CD and its one-center approximation (1C-CD) generally yields errors below 0.03 kcal/mol, whereas 10(-3)E(h) is sufficient to obtain the same level of accuracy or better with the atomic CD (aCD) and atomic compact CD (acCD) auxiliary basis sets. Comparing to commonly used predefined auxiliary basis sets, we find that while the aCD and acCD sets are larger by a factor of 2-4 with triple-zeta AO basis sets, they provide results 1-2 orders of magnitude more accurate.
  •  
22.
  • Bottaro, Sandro, et al. (författare)
  • Subtle Monte Carlo Updates in Dense Molecular Systems
  • 2012
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:2, s. 695-702
  • Tidskriftsartikel (refereegranskat)abstract
    • Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as the native state of globular proteins. Here, we introduce a kinetic algorithm, CRISP, that greatly enhances the sampling efficiency in all-atom MC simulations of dense systems. The algorithm is based on an exact analytical solution to the classic chain-closure problem, making it possible to express the interdependencies among degrees of freedom in the molecule as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater efficiency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results suggest our method as a valuable tool in the study of molecules in atomic detail, offering a potential alternative to molecular dynamics for probing long time-scale conformational transitions.
  •  
23.
  • Brand, Manuel, et al. (författare)
  • Efficient and Parallel Implementation of Real and Complex Response Functions Employing the Second-Order Algebraic-Diagrammatic Construction Scheme for the Polarization Propagator
  • 2023
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 20:1, s. 103-113
  • Tidskriftsartikel (refereegranskat)abstract
    • We present the implementation of an efficient matrix-folded formalism for the evaluation of complex response functions and the calculation of transition properties at the level of the second-order algebraic-diagrammatic construction (ADC(2)) scheme. The underlying algorithms, in combination with the adopted hybrid MPI/OpenMP parallelization strategy, enabled calculations of the UV/vis spectra of a guanine oligomer series ranging up to 1032 contracted basis functions, thereby utilizing vast computational resources from up to 32,768 CPU cores. Further analysis of the convergence behavior of the involved iterative subspace algorithms revealed the superiority of a frequency-separated treatment of response equations even for a large spectral window, including 101 frequencies. We demonstrate the applicability to general quantum mechanical operators by the first reported electronic circular dichroism spectrum calculated with a complex polarization propagator approach at the ADC(2) level of theory.
  •  
24.
  • Brumboiu, Iulia Emilia, et al. (författare)
  • Influence of Electron Correlation on the Electronic Structure and Magnetism of Transition-Metal Phthalocyanines
  • 2016
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 12:4, s. 1772-1785
  • Tidskriftsartikel (refereegranskat)abstract
    • There exists an extensive literature on the electronic structure of transition-metal phthalocyanines (TMPcs), either as single molecules or adsorbed on surfaces, where explicit intra-atomic Coulomb interactions of the strongly correlated orbitals are included in the form of a Hubbard U term. The choice of U is, to a large extent, based solely on previous values reported in the literature for similar systems. Here, we provide a systematic analysis of the influence of electron correlation on the electronic structure and magnetism of several TMPcs (MnPc, FePc, CoPc, NiPc, and CuPc). By comparing calculated results to valence-band photoelectron spectroscopy measurements, and by determining the Hubbard term from linear response, we show that the choice of U is not as straightforward and can be different for each different TMPc. This, in turn, highlights the importance of individually estimating the value of U for each system before performing any further analysis and shows how this value can influence the final results.
  •  
25.
  • Brumboiu, Iulia Emilia, et al. (författare)
  • Photoelectron Spectroscopy of Molecules Beyond the Electric Dipole Approximation
  • 2019
  • Ingår i: Journal of Chemical Theory and Computation. - : AMER CHEMICAL SOC. - 1549-9618 .- 1549-9626. ; 15:10, s. 5483-5494
  • Tidskriftsartikel (refereegranskat)abstract
    • A methodology implemented to compute photoionization cross sections beyond the electric dipole approximation using Gaussian type orbitals for the initial state and plane waves for the final state is applied to molecules of various sizes. The molecular photoionization cross sections computed for valence molecular orbitals as a function of photon energy present oscillations due to the wave-like nature of both the outgoing photoelectron and of the incoming photon. These oscillations are damped by rotational and vibrational averaging or by performing a k-point summation for the solid state case. For core orbitals, the corrections introduced by going beyond the electric dipole approximation are comparable to the atomic case. For valence orbitals, nondipole corrections to the total photoinization cross sections can reach up to 20% at photon energies above 1 keV. The corrections to the differential cross sections calculated at the magic angle are larger, reaching values between 30% and 50% for all molecules included. Our findings demonstrate that photoelectron spectroscopy, especially angle-resolved, on, e.g., molecules and clusters on surfaces, using high photon energies, must be accompanied by theories that go beyond the electric dipole approximation.
  •  
26.
  • Buslaev, Pavel, et al. (författare)
  • Best Practices in Constant pH MD Simulations : Accuracy and Sampling
  • 2022
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 18:10, s. 6148-6160
  • Tidskriftsartikel (refereegranskat)abstract
    • Various approaches have been proposed to include the effect of pH in molecular dynamics (MD) simulations. Among these, the A-dynamics approach proposed by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys. 1996, 105, 2414-2423] can be performed with little computational overhead and hfor each typeence be used to routinely perform MD simulations at microsecond time scales, as shown in the accompanying paper [Aho, N. et al. J. Chem. Theory Comput. 2022, DOI: 10.1021 /acs.jctc.2c00516]. At such time scales, however, the accuracy of the molecular mechanics force field and the parametrization becomes critical. Here, we address these issues and provide the community with guidelines on how to set up and perform long time scale constant pH MD simulations. We found that barriers associated with the torsions of side chains in the CHARMM36m force field are too high for reaching convergence in constant pH MD simulations on microsecond time scales. To avoid the high computational cost of extending the sampling, we propose small modifications to the force field to selectively reduce the torsional barriers. We demonstrate that with such modifications we obtain converged distributions of both protonation and torsional degrees of freedom and hence consistent pK(a) estimates, while the sampling of the overall configurational space accessible to proteins is unaffected as compared to normal MD simulations. We also show that the results of constant pH MD depend on the accuracy of the correction potentials. While these potentials are typically obtained by fitting a low-order polynomial to calculated free energy profiles, we find that higher order fits are essential to provide accurate and consistent results. By resolving problems in accuracy and sampling, the work described in this and the accompanying paper paves the way to the widespread application of constant pH MD beyond pK(a) prediction.
  •  
27.
  • Buslaev, Pavel, et al. (författare)
  • Scalable Constant pH Molecular Dynamics in GROMACS
  • 2022
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 18:10, s. 6148-6160
  • Tidskriftsartikel (refereegranskat)abstract
    • Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414–2423] was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to the poor scaling of that code with respect to the number of titratable sites. To overcome this limitation, we implemented an alternative scheme for interpolating the Hamiltonians of the protonation states that makes the constant pH molecular dynamics simulations almost as fast as a normal MD simulation with GROMACS. In addition, we implemented a simpler scheme, called multisite representation, for modeling side chains with multiple titratable sites, such as imidazole rings. This scheme, which is based on constraining the sum of the λ-coordinates, not only reduces the complexity associated with parametrizing the intramolecular interactions between the sites but also is easily extendable to other molecules with multiple titratable sites. With the combination of a more efficient interpolation scheme and multisite representation of titratable groups, we anticipate a rapid uptake of constant pH molecular dynamics simulations within the GROMACS user community.
  •  
28.
  • Bäcktorp, Carina, 1964, et al. (författare)
  • Mechanism of Air Oxidation of the Fragrance Terpene Geraniol
  • 2008
  • Ingår i: J.Chem.Theory Comput.. - : American Chemical Society (ACS). ; 4, s. 101-106
  • Tidskriftsartikel (refereegranskat)abstract
    • The fragrance terpene geraniol autoxidizes upon air exposure and forms a mixture of oxidation products, some of which are skin sensitizers. Reactions of geraniol with O2 have been studied with DFT (B3LYP) and the computational results compared to experimentally observed product ratios. The oxidation is initiated by hydrogen abstraction, forming an allylic radical which combines with an O2 molecule to yield an intermediate peroxyl radical. In the subsequent step, geraniol differs from previously studied cases, in which the radical chain reaction is propagated through intermolecular hydrogen abstraction. The hydroxy-substituted allylic peroxyl radical prefers an intramolecular rearrangement, producing observable aldehydes and the hydroperoxyl radical, which in turn can propagate the radical reaction. Secondary oxidation products like epoxides and formates were also considered, and plausible reaction pathways for formation are proposed.
  •  
29.
  • Caleman, Carl, et al. (författare)
  • Force Field Benchmark of Organic Liquids : Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant
  • 2012
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:1, s. 61-74
  • Tidskriftsartikel (refereegranskat)abstract
    • The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys. 2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed expose of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem. 2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.
  •  
30.
  • Cammi, Roberto, et al. (författare)
  • Varying Electronic Configurations in Compressed Atoms: From the Role of the Spatial Extension of Atomic Orbitals to the Change of Electronic Configuration as an Isobaric Transformation
  • 2020
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9626 .- 1549-9618. ; 16:8, s. 5047-5056
  • Tidskriftsartikel (refereegranskat)abstract
    • A quantum chemical model for the study of the electronic structure of compressed atoms lends itself to a perturbation-theoretic analysis. It is shown, both analytically and numerically, that the increase of the electronic energy with increasing compression depends on the electronic configuration, as a result of the variable spatial extent of the atomic orbitals involved. The different destabilization of the electronic states may lead to an isobaric change of the ground-state electronic configuration, and the same first-order model paves the way to a simple thermodynamical interpretation of this process.
  •  
31.
  • Cao, Lili, et al. (författare)
  • Protonation and Reduction of the FeMo Cluster in Nitrogenase Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations
  • 2018
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 14:12, s. 6653-6678
  • Tidskriftsartikel (refereegranskat)abstract
    • We have performed a systematic computational study of the relative energies of possible protonation states of the FeMo cluster in nitrogenase in the E0-E4 states, i.e., the resting state and states with 1-4 electrons and protons added but before N2 binds. We use the combined quantum mechanics and molecular mechanics (QM/MM) approach, including the complete solvated heterotetrameric enzyme in the calculations. The QM system consisted of 112 atoms, i.e., the full FeMo cluster, as well all groups forming hydrogen bonds to it within 3.5 Å. It was treated with either the TPSS-D3 or B3LYP-D3 methods with the def2-SV(P) or def2-TZVPD basis sets. For each redox state, we calculated relative energies of at least 50 different possible positions for the proton, added to the most stable protonation state of the level with one electron less. We show quite conclusively that the resting E0 state is not protonated using quantum refinement and by comparing geometries to the crystal structure. The E1 state is protonated on S2B, in agreement with most previous computational studies. However, for the E2-E4 states, the two QM methods give diverging results, with relative energies that differ by over 300 kJ/mol for the most stable E4 states. TPSS favors hydride ions binding to the Fe ions. The first bridges Fe2 and Fe6, whereas the next two bind terminally to either Fe4, Fe5, or Fe6 with nearly equal energies. On the other hand, B3LYP disfavors hydride ions and instead suggests that 1-3 protons bind to the central carbide ion.
  •  
32.
  • Cao, Lili, et al. (författare)
  • What Is the Structure of the E4 Intermediate in Nitrogenase?
  • 2020
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 16, s. 1936-1952
  • Tidskriftsartikel (refereegranskat)abstract
    • Nitrogenase is the only enzyme that can cleave the strong triple bond inN2. The active site contains a complicated MoFe7S9C cluster. It is believed that itneeds to accept four protons and electrons, forming the E4 state, before it can bind N2.However, there is no consensus on the atomic structure of the E4 state. Experimentalstudies indicate that it should contain two hydride ions bridging two pairs of Fe ions,and it has been suggested that both hydride ions as well as the two protons bind on thesame face of the cluster. On the other hand, density functional theory (DFT) studieshave indicated that it is energetically more favorable with either three hydride ions or with a triply protonated carbide ion, depending on the DFT functional. We have performed a systematic combined quantum mechanical and molecular mechanical (QM/MM) study of possible E4 states with two bridging hydride ions. Our calculations suggest that the most favorable structure has hydride ions bridging the Fe2/6 and Fe3/7 ion pairs. In fact, such structures are 14 kJ/mol more stable than structures with three hydride ions, showing that pure DFT functionals give energetically most favorable structures in agreement with experiments. An important reason for this finding is that we have identified a new type of broken-symmetry state that involves only two Fe ions with minority spin, in contrast to the previously studied states with three Fe ions with minority spin. The energetically best structures have the two hydride ions on different faces of the FeMo cluster, whereas better agreement with ENDOR data is obtained if they are on the same face; such structures are only 6−22 kJ/mol less stable.
  •  
33.
  • Chaudhuri, Subhajyoti, et al. (författare)
  • Electron Transfer Assisted by Vibronic Coupling from Multiple Modes
  • 2017
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 13:12, s. 6000-6009
  • Tidskriftsartikel (refereegranskat)abstract
    • Understanding the effect of vibronic coupling on electron transfer (ET) rates is a challenge common to a wide range of applications, from electrochemical synthesis and catalysis to biochemical reactions and solar energy conversion. The Marcus-Jortner-Levich (MJL) theory offers a model of ET rates based on a simple analytic expression with a few adjustable parameters. However, the MJL equation in conjunction with density functional theory (DFT) has yet to be established as a predictive first-principles methodology. A framework is presented for calculating transfer rates modulated by molecular vibrations, that circumvents the steep computational cost which has previously necessitated approximations such as condensing the vibrational manifold into a single empirical frequency. Our DFT MJL approach provides robust and accurate predictions of ET rates spanning over 4 orders of magnitude in the 10(6)-10(10) s(-1) range. We evaluate the full MJL equation with a Monte Carlo sampling of the entire active space of thermally accessible vibrational modes, while using no empirical parameters. The contribution to the rate of individual modes is illustrated, providing insight into the interplay between vibrational degrees of freedom and changes in electronic state. The reported findings are valuable for understanding ET rates modulated by multiple vibrational modes, relevant to a broad range of systems within the chemical sciences.
  •  
34.
  • Chaudret, Robin, et al. (författare)
  • Revisiting H2O Nucleation around Au+ and Hg2+ : The Peculiar "Pseudo-Soft" Character of the Gold Cation
  • 2014
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 10:5, s. 1900-1909
  • Tidskriftsartikel (refereegranskat)abstract
    • In this contribution, we propose a deeper understanding of the electronic effects affecting the nucleation of water around the Au+ and Hg2+ metal cations using quantum chemistry. To do so, and in order to go beyond usual energetical studies, we make extensive use of state of the art quantum interpretative techniques combining ELF/NCI/QTAIM/EDA computations to capture all ranges of interactions stabilizing the well characterized microhydrated structures. The Electron Localization Function (ELF) topological analysis reveals the peculiar role of the Au+ outer-shell core electrons (subvalence) that appear already spatially preorganized once the addition of the first water molecule occurs. Thus, despite the addition of other water molecules, the electronic structure of Au(H2O)(+) appears frozen due to relativistic effects leading to a maximal acceptation of only two waters in gold's first hydration shell. As the values of the QTAIM (Quantum Theory of Atoms in Molecules) cations's charge is discussed, the Non Covalent Interactions (NCI) analysis showed that Au+ appears still able to interact through longer range van der Waals interaction with the third or fourth hydration shell water molecules. As these types of interaction are not characteristic of either a hard or soft metal cation, we introduced the concept of a "pseudo-soft" cation to define Au+ behavior. Then, extending the study, we performed the same computations replacing Au+ with Hg2+, an isoelectronic cation. If Hg2+ behaves like Au+ for small water clusters, a topological, geometrical, and energetical transition appears when the number of water molecules increases. Regarding the HSAB theory, this transition is characteristic of a shift of Hg2+ from a pseudosoft form to a soft ion and appears to be due to a competition between the relativistic and correlation effects. Indeed, if relativistic effects are predominant, then mercury will behave like gold and have a similar subvalence/geometry; otherwise when correlation effects are predominant, Hg2+ behaves like a soft cation.
  •  
35.
  • Chen, Mo, et al. (författare)
  • Molecular Dynamics Simulations of the Ionic Liquid 1-n-Butyl-3-Methylimidazolium Chloride and Its Binary Mixtures with Ethanol
  • 2014
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 10:10, s. 4465-4479
  • Tidskriftsartikel (refereegranskat)abstract
    • Room temperature ionic liquids (ILs) of the imidazolium family have attracted much attention during the past decade for their capability to dissolve biomass. Besides experimental work, numerous compuational studies have been concerned with the physical properties of both neat ILs and their interactions with different solutes, in particular, carbohydrates. Many classical force fields designed specifically for ILs have been found to yield viscosities that are too high for the liquid state, which has been attributed to the fact that the effective charge densities are too high due to the lack of electronic polarizability. One solution to this problem has been uniform scaling of the partial charges by a scale factor in the range 0.6-0.9, depending on model. This procedure has been shown to improve the viscosity of the models, and also to positively affect other properties, such as diffusion constants and ionic conductivity. However, less attention has been paid to how this affects the overall thermodynamics of the system, and the problems it might create when the IL models are combined with other force fields (e.g., for solutes). In the present work, we employ three widely used IL force fields to simulate 1-n-buty1-3-methyl-imidazolium chloride in both the crystal and the liquid state, as well as its binary mixture with ethanol. Two approaches are used: one in which the ionic charge is retained at its full integer value and one in which the partial charges are uniformly reduced to 85%. We investigate and calculate crystal and liquid structures, molar heat capacities, heats of fusion, self-diffusion constants, ionic conductivity, and viscosity for the neat IL, and ethanol activity as a function of ethanol concentration for the binary mixture. We show that properties of the crystal are less affected by charge scaling compared to the liquid. In the liquid state, transport properties of the neat IL are generally improved by scaling, whereas values for the heat of fusion are unaffected, and results for the heat capacity are ambiguous. Neither full nor reduced charges could reproduce experimental ethanol activities for the whole range of compositions.
  •  
36.
  • Chen, Shu-Feng, et al. (författare)
  • Chemiluminescence of Coelenterazine and Fluorescence of Coelenteramide : A Systematic Theoretical Study
  • 2012
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:8, s. 2796-2807
  • Tidskriftsartikel (refereegranskat)abstract
    • A systematic investigation of the structural and spectroscopic properties of coelenteramide has been performed at the TD-CAM-B3LYP/6-31+G(d,p) level of theory, including various fluorescence and chemiluminescence states. The influence of geometric conformations, solvent polarity, protonation state, and the covalent character of the O-H bond of the hydroxyphenyl moiety were carefully studied. Striking differences in geometries and electronic structures among the states responsible for light emission were characterized. All fluorescence states can be described as a limited charge transfer process for a planar amide moiety. However, the chemiluminescence state is characterized by a much larger charge transfer that takes place over a longer distance. Moreover, the chemiluminescent coelenteramide structure exhibits an amide moiety that is no longer planar, in agreement with recent, more accurate ab initio results [Roca-Sanjuan et al J. Chem. Theory Comput. 2011, 7, 4060] Because the chemiluminescence state appears to be completely dark, a new mechanism is tentatively introduced for this process.
  •  
37.
  • Chen, Shu-Feng, et al. (författare)
  • Systematic theoretical investigation on the light emitter of firefly
  • 2011
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 7:3, s. 798-803
  • Tidskriftsartikel (refereegranskat)abstract
    • This is a systematic theoretical investigation on all the possible light emitters of firefly using multireference method. Six chemical forms of oxyluciferin (OxyLH2) molecules/anions were studied by a multi-state complete active space second order perturbation (MS-CASPT2) method in vacuum and DMSO. The calculated results and subsequent analysis excluded enol-OxyLH2, keto-OxyLH2 and enolate-OxyLH- as possible light emitters. The remaining three candidates, phenolate-enol-OxyLH-, phenolate-keto-OxyLH- and OxyL2-, were further investigated in protein by a MS-CASPT2/molecular mechanics (MM) study to explain the natural bioluminescence of firefly. By comparison of the MS-CASPT2/MM calculated results of phenolate-enol-OxyLH-, phenolate-keto-OxyLH- and OxyL2- with the experimental observation and detailed analysis, we concluded that the direct decomposition excited-state product of firefly dioxetanone in vivo and the only light emitter of firefly in natural bioluminescence is the first singlet exited state (S1) of phenolate-keto-OxyLH-.
  •  
38.
  • Cordomi, Arnau, et al. (författare)
  • Effect of Force Field Parameters on Sodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers
  • 2009
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 5:8, s. 2125-2134
  • Tidskriftsartikel (refereegranskat)abstract
    • The behavior of electrolytes in molecular dynamics simulations of zwitterionic phospholipid bilayers; is very sensitive to the force field parameters used. Here, several 200 ns molecular dynamics of simulations of dipalmitoyl phosphotidylcholine (PC) bilayers in 0.2 M sodium or potassium chloride using various common force field parameters for the cations are presented. All employed parameter sets give a larger number of Na+ ions than K+ ions that bind to the lipid heads, but depending on the parameter choice quite different results are seen. A wide range of coordination numbers for the Na+ and K+ ions is also observed. These findings have been analyzed and compared to published experimental data. Some simulations produce aggregates of potassium chloride, indicating (in accordance with published simulations) that these force fields do not reproduce the delicate balance between salt and solvated ions. The differences between the force fields can be characterized by one single parameter, the electrostatic radius of the ion, which is correlated to sigma(MO) (M represents Na+/K+), the Lennard-Jones radius. When this parameter exceeds a certain threshold, binding to the lipid heads is no longer observed. One would, however, need more accurate experimental data to judge or rank the different force fields precisely. Still, reasons for the poor performance of some of the parameter sets are clearly demonstrated, and a quality control. procedure is provided.
  •  
39.
  • Coriani, Sonia, et al. (författare)
  • Asymmetric-Lanczos-Chain-Driven Implementation of Electronic Resonance Convergent Coupled-Cluster Linear Response Theory
  • 2012
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society. - 1549-9618 .- 1549-9626. ; 8:5, s. 1616-1628
  • Tidskriftsartikel (refereegranskat)abstract
    • We present an implementation of the damped coupled-cluster linear response function based on an asymmetric Lanczos chain algorithm for the hierarchy of coupled-cluster approximations CCS (coupled-cluster singles), CC2 (coupled. cluster singles and approximate doubles), and CCSD (coupled-cluster singles and doubles). Triple corrections to the excitation energies can be included via the CCSDR(3) (coupled-cluster singles and doubles with noniterative-triples-corrected excitation energies) approximation. The performance and some of the potentialities of the approach are investigated in calculations of the visible/ultraviolet absorption spectrum and the dispersion of the real polarizability in near-resonant regions of pyrimidine, the near-edge absorption fine structure (NEXAFS) of ammonia, and the direct determination of the C-6 dipole-dipole dispersion coefficient of the benzene dimer.
  •  
40.
  • Creutzberg, Joel, et al. (författare)
  • Polarizable Embedding Complex Polarization Propagator in Four- and Two-Component Frameworks
  • 2022
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 18:6, s. 3671-3686
  • Tidskriftsartikel (refereegranskat)abstract
    • Explicit embedding methods combined with the complex polarization propagator (CPP) enable the modeling of spectroscopy for increasingly complex systems with a high density of states. We present the first derivation and implementation of the CPP in four- and exact-two-component (X2C) polarizable embedding (PE) frameworks. We denote the developed methods PE-4c-CPP and PE-X2C-CPP, respectively. We illustrate the methods by estimating the solvent effect on ultraviolet-visible (UV-vis) and X-ray atomic absorption (XAS) spectra of [Rh(H2O)6]3+ and [Ir(H2O)6]3+ immersed in aqueous solution. We moreover estimate solvent effects on UV-vis spectra of a platinum complex that can be photochemically activated (in water) to kill cancer cells. Our results clearly show that the inclusion of the environment is required: UV-vis and (to a lesser degree) XAS spectra can become qualitatively different from vacuum calculations. Comparison of PE-4c-CPP and PE-X2C-CPP methods shows that X2C essentially reproduces the solvent effect obtained with the 4c methods.
  •  
41.
  • Cuéllar-Zuquin, Juliana, et al. (författare)
  • Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size
  • 2023
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:22, s. 8258-8272
  • Tidskriftsartikel (refereegranskat)abstract
    • We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1nO/Nπ* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.
  •  
42.
  • Dahlberg, Martin, 1979-, et al. (författare)
  • Mechanical properties of coarse grained bilayers formed by cardiolipin and zwitterionic lipids
  • 2010
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 6:5, s. 1638-1649
  • Tidskriftsartikel (refereegranskat)abstract
    • Lipid shape and charge are connected with the physical properties and biological function of membranes. Cardiolipin, a double phospholipid with four chains and the potential of changing its charge with pH, is crucially connected with mitochondrial inner membrane shape, and recent experiments suggest that local pH changes allow highly curved local geometries. Here, we use a coarse grained molecular dynamics model to investigate the mechanical properties of cardiolipin bilayers, systematically varying the headgroup charge and composition in mixtures with zwitterionic DOPC or DOPE. Low cardiolipin charge, corresponding to low pH, was found to induce bending moduli on the order of kBT, and curved microdomains. On the length scale investigated, in contrast to continuum theoretical models, we found the area modulus and bending modulus to be inversely correlated for mixtures of cardiolipin and DOPC/DOPE, explainable by changes in the effective head group volume.
  •  
43.
  • Daku, Latevi Max Lawson, et al. (författare)
  • Accurate Spin-State Energetics of Transition Metal Complexes. 1. CCSD(T), CASPT2, and DFT Study of [M(NCH)(6)](2+) (M = Fe, Co)
  • 2012
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:11, s. 4216-4231
  • Tidskriftsartikel (refereegranskat)abstract
    • Highly accurate estimates of the high-spin/low-spin energy, difference Delta E-HL(el) in the high-spin complexes [Fe(NCH)(6)](2+) and [Co(NCH)(6)](2+) have been obtained from the results of CCSD(T) calculations extrapolated to the complete basis set limit. These estimates are shown to be strongly influenced by scalar relativistic effects. They have been used to assess the performances of the CASPT2 method and 30 density functionals of the GGA, meta-GGA, global hybrid, RSH, and double-hybrid types. For the CASPT2 method, the results of the assessment support the proposal [Kepenekian, M.; Robert, V.; Le Guennic, B. J. Chem. Phys. 2009, 131, 114702] that the ionization potential-electron affinity (IPEA) shift defining the zeroth-order Hamiltonian be raised from its standard value of 0.25 au to 0.50-0.70 au for the determination of Delta E-HL(el) in Fe(II) complexes with a [FeN6] core. At the DFT level, some of the assessed functionals proved to perform within chemical accuracy (+/- 350 cm(-1)) for the spin-state energetics of [Fe(NCH)(6)](2+), others for that of [Co(NCH)(6)](2+), but none of them simultaneously for both complexes. As demonstrated through a reparametrization of the CAM-PBEO range-separated hybrid, which led to a functional that performs within chemical accuracy for the spin-state energetics of both complexes, performing density functionals of broad applicability may be devised by including in their training sets highly accurate data like those reported here for [Fe(NCH)(6)](2+) and [Co(NCH)(6)](2+).
  •  
44.
  • Darre, L., et al. (författare)
  • Molecular Dynamics Simulations and Neutron Reflectivity as an Effective Approach To Characterize Biological Membranes and Related Macromolecular Assemblies
  • 2015
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 11:10, s. 4875-4884
  • Tidskriftsartikel (refereegranskat)abstract
    • In combination with other spectroscopy, microscopy, and scattering techniques, neutron reflectivity is a powerful tool to characterize biological systems. Specular reflection of neutrons provides structural information at the nanometer and subnanometer length scales, probing the composition and organization of layered materials. Currently, analysis of neutron reflectivity data involves several simplifying assumptions about the structure of the sample under study, affecting the extraction and interpretation of information from the experimental data. Computer simulations can be used as a source of structural and dynamic data with atomic resolution. We present a novel tool to compare the structural properties determined by neutron reflectivity experiments with those obtained from molecular simulations. This tool allows benchmarking the ability of molecular dynamics simulations to reproduce experimental data, but it also promotes unbiased interpretation of experimentally determined quantities. Two application examples are presented to illustrate the capabilities of the new tool. The first example is the generation of reflectivity profiles for a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer from molecular dynamics simulations using data from both atomistic and coarse-grained models, and comparison with experimentally measured data. The second example is the calculation of lipid volume changes with temperature and composition from all atoms simulations of single and mixed 1,2-di-palmitoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (DPPC) bilayers.
  •  
45.
  • Das, Susanta, et al. (författare)
  • Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical–Molecular Mechanical Simulations of Proton Transfer in DNA
  • 2018
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 14:3, s. 1695-1705
  • Tidskriftsartikel (refereegranskat)abstract
    • In recent years, a number of quantum mechanical-molecular mechanical (QM/MM) enzyme studies have investigated the dependence of reaction energetics on the size of the QM region using energy and free energy calculations. In this study, we revisit the question of QM region size dependence in QM/MM simulations within the context of energy and free energy calculations using a proton transfer in a DNA base pair as a test case. In the simulations, the QM region was treated with a dispersion-corrected AM1/d-PhoT Hamiltonian, which was developed to accurately describe phosphoryl and proton transfer reactions, in conjunction with an electrostatic embedding scheme using the particle-mesh Ewald summation method. With this rigorous QM/MM potential, we performed rather extensive QM/MM sampling, and found that the free energy reaction profiles converge rapidly with respect to the QM region size within ca. +/- 1 kcal/mol. This finding suggests that the strategy of QM/MM simulations with reasonably sized and selected QM regions, which has been employed for over four decades, is a valid approach for modeling complex biomolecular systems. We point to possible causes for the sensitivity of the energy and free energy calculations to the size of the QM region, and potential implications.
  •  
46.
  • De Gracia Triviño, Juan Angel, et al. (författare)
  • Complete Active Space Methods for NISQ Devices: The Importance of Canonical Orbital Optimization for Accuracy and Noise Resilience
  • 2023
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:10, s. 2863-2872
  • Tidskriftsartikel (refereegranskat)abstract
    • To avoid the scaling of the number of qubits with the size of the basis set, one can divide the molecular space into active and inactive regions, which is also known as complete active space methods. However, selecting the active space alone is not enough to accurately describe quantum mechanical effects such as correlation. This study emphasizes the importance of optimizing the active space orbitals to describe correlation and improve the basis-dependent Hartree-Fock energies. We will explore classical and quantum computation methods for orbital optimization and compare the chemically inspired ansatz, UCCSD, with the classical full CI approach for describing the active space in both weakly and strongly correlated molecules. Finally, we will investigate the practical implementation of a quantum CASSCF, where hardware-efficient circuits must be used and noise can interfere with accuracy and convergence. Additionally, we will examine the impact of using canonical and noncanonical active orbitals on the convergence of the quantum CASSCF routine in the presence of noise.
  •  
47.
  • De Vico, Luca, et al. (författare)
  • Location of Two Seams in the Proximity of the C-2v pi pi Minimum Energy Path of Formaldehyde
  • 2009
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 5:1, s. 186-191
  • Tidskriftsartikel (refereegranskat)abstract
    • Photochemical reactions rationalization is a key aspect for the understanding and setup of novel experiment and novel photoinitiated pathways. In this respect, the relationship between minimum energy paths over an excited-state and the intersection to lower potential energy surfaces is fundamental. In order to help the understanding of this relationship, in this study we present a novel kind of constraint for geometry optimizations, namely, an “orthogonality” constraint. Its possible applications are described. A complete example on how to retrieve the direct relationship between a minimum energy path over an excited-state potential energy surface and a conical intersection seam is given for C-2v symmetry constrained formaldehyde. The advantages of using the novel constraint when rationalizing a (photo)chemical reaction are presented.
  •  
48.
  • De Vico, Luca, et al. (författare)
  • New general tools for constrained geometry optimizations
  • 2005
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 1:5, s. 1029-1037
  • Tidskriftsartikel (refereegranskat)abstract
    • A modification of the constrained geometry optimization method by Anglada and Bofill (Anglada, J. M.; Bofill, J. M. J. Comput. Chem. 1997, 18, 992-1003) is designed and implemented. The changes include the choice of projection, quasi-line-search, and the use of a Rational Function optimization approach rather than a reduced-restricted-quasi-Newton-Raphson method in the optimization step. Furthermore, we show how geometrical constrains can be implemented in an approach based on nonreclunclant curvilinear coordinates avoiding the inclusion of the constraints in the set of redundant coordinates used to define the internal coordinates. The behavior of the new implementation is demonstrated in geometry optimizations featuring single or multiple geometrical constraints (bond lengths, angles, etc.), optimizations on hyperspherical cross sections (as in the computation of steepest descent paths), and location of energy minima on the intersection subspace of two potential energy surfaces (i.e. minimum energy crossing points). In addition, a novel scheme to determine the crossing point geometrically nearest to a given molecular structure is proposed.
  •  
49.
  • Di Palma, Francesco, et al. (författare)
  • Probing Interplays between Human XBP1u Translational Arrest Peptide and 80S Ribosome
  • 2022
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 18:3, s. 1905-1914
  • Tidskriftsartikel (refereegranskat)abstract
    • The ribosome stalling mechanism is a crucial biological process, yet its atomistic underpinning is still elusive. In this framework, the human XBP1u translational arrest peptide (AP) plays a central role in regulating the unfolded protein response (UPR) in eukaryotic cells. Here, we report multimicrosecond all-atom molecular dynamics simulations designed to probe the interactions between the XBP1u AP and the mammalian ribosome exit tunnel, both for the wild type AP and for four mutant variants of different arrest potencies. Enhanced sampling simulations allow investigating the AP release process of the different variants, shedding light on this complex mechanism. The present outcomes are in qualitative/quantitative agreement with available experimental data. In conclusion, we provide an unprecedented atomistic picture of this biological process and clear-cut insights into the key AP-ribosome interactions.
  •  
50.
  • Dias, Roberta P., et al. (författare)
  • Outer Membrane Remodeling : The Structural Dynamics and Electrostatics of Rough Lipopolysaccharide Chemotypes
  • 2014
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 10:6, s. 2488-2497
  • Tidskriftsartikel (refereegranskat)abstract
    • Lipopolysaccharides (LPS) are the primary constituent of the outer membrane of Gram-negative bacteria such as Pseudomonas aeruginosa. Gram-negative bacteria can synthesize modified forms of LPS in response to environmental stimuli or due to genetic mutations, a process known as outer membrane remodeling. Chemical modifications of the LPS modulate the integrity and antibiotic susceptibility of bacterial outer membranes. It also governs microbial adhesion to tissues and artificial material surfaces. We have extended a previous model of the rough LPS to include four novel chemotypes rmlC, galU, LPS Re, and Lipid-A. Atomistic molecular dynamics (MD) simulations were performed for outer membrane models constituted of each LPS chemotypes and 1,2-dipalmitoyl-3-phosphatidylethanolamine. It is shown that the decrease in the LPS polysaccharide chain length leads to a significant increase in the diffusion coefficients for the Ca2+ counterions, increase in acyl chain packing (decrease in membrane fluidity), and attenuation of the negative potential across the LPS surface as positive counterions becomes more exposed to the solvent. The electrostatic potential on the LPS surfaces reflects heterogeneous charge distributions with increasingly larger patches of positive and negative potentials as the polysaccharide chain length decreases. Such a pattern originates from the spatial arrangement of charged phosphate-Ca2+ clusters in the LPS inner-core that becomes exposed in the membrane surface as monosaccharide units are lost in the shortest chemotypes LPS Re and Lipid-A. These MD-derived conformational ensembles reproduce experimental trends and provide atom-level structural information on the rough LPS chemotypes that can help to rationalize antibiotic resistance and bacterial adhesion processes.
  •  
Skapa referenser, mejla, bekava och länka
  • Resultat 1-50 av 287
Typ av publikation
tidskriftsartikel (286)
forskningsöversikt (1)
Typ av innehåll
refereegranskat (286)
populärvet., debatt m.m. (1)
Författare/redaktör
Ryde, Ulf (29)
Ågren, Hans (17)
van Der Spoel, David (14)
Lindh, Roland (14)
Kongsted, Jacob (13)
Aquilante, Francesco (11)
visa fler...
Rinkevicius, Zilvina ... (10)
Norman, Patrick (10)
Lindh, Roland, Profe ... (10)
Rubensson, Emanuel H ... (9)
Lundberg, Marcus, 19 ... (8)
Söderhjelm, Pär (8)
Åqvist, Johan (8)
Fernández Galván, Ig ... (8)
Roca-Sanjuán, Daniel (8)
Nilsson, L. (7)
Hess, Berk (7)
Li, Xin (7)
Lindh, Roland, 1958- (7)
Skepö, Marie (7)
Genheden, Samuel (7)
Dreuw, Andreas (7)
Ferre, Nicolas (6)
Olivucci, Massimo (6)
Nam, Kwangho (6)
Delcey, Mickael G, 1 ... (6)
Norrby, Per-Ola, 196 ... (5)
Lyubartsev, Alexande ... (5)
Coriani, Sonia (5)
Lindahl, Erik (5)
Rahm, Martin, 1982 (5)
Gagliardi, Laura (5)
Rudberg, Elias (5)
Fransson, Thomas (5)
van Maaren, Paul J. (5)
Natarajan Arul, Muru ... (4)
Veryazov, Valera (4)
Vahtras, Olav (4)
Laaksonen, Aatto (4)
Salek, Pawel (4)
Boström, Jonas (4)
Pedersen, Thomas Bon ... (4)
Vacher, Morgane (4)
Murugan, N. Arul (4)
Eriksson, Leif A. (4)
Niklasson, Anders M. ... (4)
Navizet, Isabelle (4)
Liu, Ya-Jun (4)
Edholm, Olle (4)
Raggi, Gerardo (4)
visa färre...
Lärosäte
Uppsala universitet (99)
Lunds universitet (71)
Kungliga Tekniska Högskolan (68)
Stockholms universitet (42)
Linköpings universitet (12)
Chalmers tekniska högskola (12)
visa fler...
Umeå universitet (11)
Karolinska Institutet (10)
Göteborgs universitet (9)
Örebro universitet (5)
Högskolan i Gävle (1)
Mittuniversitetet (1)
Linnéuniversitetet (1)
Karlstads universitet (1)
Sveriges Lantbruksuniversitet (1)
visa färre...
Språk
Engelska (287)
Forskningsämne (UKÄ/SCB)
Naturvetenskap (259)
Teknik (6)
Medicin och hälsovetenskap (2)

År

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.

 
pil uppåt Stäng

Kopiera och spara länken för att återkomma till aktuell vy