| 1. |
- Allnér, Olof, et al.
(författare)
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Magnesium ion–water coordination and exchange in biomolecular simulations
- 2012
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Ingår i: Journal of Chemical Theory and Computation. - Stockholm : Karolinska Institutet, Dept of Biosciences and Nutrition. - 1549-9618 .- 1549-9626.
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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.
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| 2. |
- Abraham, Mark J, et al.
(författare)
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Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations
- 2008
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 4:7
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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.
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| 3. |
- Aho, Noora, et al.
(författare)
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Scalable Constant pH Molecular Dynamics in GROMACS
- 2022
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 18:10, s. 6148-6160
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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.
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| 4. |
- Ali, Md Ehesan, et al.
(författare)
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Designing the Redox-Driven Switching of Ferro- to Antiferromagnetic Couplings in Organic Diradicals
- 2013
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 9:12, s. 5216-5220
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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.
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| 5. |
- Almlöf, Martin, et al.
(författare)
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Improving the accuracy of the linear interaction energy method for solvation free energies
- 2007
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 3:6, s. 2162-2175
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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.
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| 6. |
- Ammothum Kandy, Akshay Krishna, et al.
(författare)
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Curvature Constrained Splines for DFTB Repulsive Potential Parametrization
- 2021
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 17:3, s. 1771-1781
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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.
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| 7. |
- Aquilante, Francesco, et al.
(författare)
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Cholesky decomposition-based multiconfiguration second-order perturbation theory (CD-CASPT2) : application to the spin-state energetics of Co-III(diiminato)(NPh).
- 2008
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 4:5, s. 694-702
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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.
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| 8. |
- Badri, Zahra, et al.
(författare)
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All-Metal Aromaticity : Revisiting the Ring Current Model among Transition Metal Clusters
- 2013
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 9:11, s. 4789-4796
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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.
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| 9. |
- Barcza, Gergely, et al.
(författare)
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DMRG on Top of Plane-Wave Kohn-Sham Orbitals: A Case Study of Defected Boron Nitride
- 2021
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Ingår i: Journal of Chemical Theory and Computation. - : AMER CHEMICAL SOC. - 1549-9618 .- 1549-9626. ; 17:2, s. 1143-1154
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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.
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| 10. |
- Barucha-Dobrautz, Werner, 1987, et al.
(författare)
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Toward Real Chemical Accuracy on Current Quantum Hardware Through the Transcorrelated Method
- 2024
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Ingår i: Journal of Chemical Theory and Computation. - 1549-9626 .- 1549-9618. ; 20:10, s. 4146-4160
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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.
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