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Special Issue "Combined Quantum Mechanical and Molecular Mechanical Methods and Simulations"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Theoretical Chemistry".

Deadline for manuscript submissions: closed (7 September 2018)

Special Issue Editors

Guest Editor
Prof. Hai Lin

University of Colorado Denver, Denver, CO 80217, USA
Website | E-Mail
Interests: multi-scale modeling; combined QM/MM; ion solvation and transport; membrane proteins; enzymatic reactions
Guest Editor
Prof. Dr. Donald G. Truhlar

Department of Chemistry, Chemical Theory Center, Inorganometallic Catalyst Design Center, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
Website | E-Mail
Interests: chemical dynamics; catalysis; photochemistry; molecular modeling; computational thermodyanmics; electronic structure theory

Special Issue Information

Dear Colleagues,

Combined quantum-mechanics/molecular-mechanics (QM/MM) is an important component of many methods for in multi-scale modelling and simulations. The algorithms involve partitioning an entire system into a small subsystem of primary interest, which is modeled by an accurate QM level of theory, and the surroundings that interact with it, which are treated by MM force fields for computational efficiency. The surroundings may include the less active part of a large molecule, the solvent, all or part of a protein, or more than one of these—or other possibilities. The integration of QM and MM methods makes it affordable to realistically describe reactions in complex environments. QM/MM has found applications in many research fields such as enzymatic reactions and other catalytic reactions, ion solvation and transport, photochemistry, nanostructured materials, etc.

This Special Issue of Molecules, “Combined Quantum Mechanical and Molecular Mechanical Methods and Simulations,” presents both recent developments and applications in this exciting field.

Prof. Hai Lin
Prof. Dr. Donald G. Truhlar
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • embedding theory and calculations
  • enzyme catalysis
  • heterogeneous catalysis
  • molecular mechanics
  • multi-scale modeling
  • photochemistry
  • polarization
  • quantum mechanics
  • reaction dynamics
  • solvation and transport

Published Papers (5 papers)

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Research

Open AccessArticle Exploring Peptide–Solvent Interactions: A Computational Study
Molecules 2018, 23(9), 2355; https://doi.org/10.3390/molecules23092355
Received: 20 August 2018 / Revised: 6 September 2018 / Accepted: 10 September 2018 / Published: 14 September 2018
PDF Full-text (5467 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The dilemma of reconciling the contradictory evidence regarding the conformation of long solvated peptide chains is the so-called “reconciliation problem”. Clues regarding the stability of certain conformations likely lie in the electronic structure at the peptide–solvent interface, but the peptide–solvent interaction is not
[...] Read more.
The dilemma of reconciling the contradictory evidence regarding the conformation of long solvated peptide chains is the so-called “reconciliation problem”. Clues regarding the stability of certain conformations likely lie in the electronic structure at the peptide–solvent interface, but the peptide–solvent interaction is not fully understood. Here, we study the influence of aqueous solvent on peptide conformations by using classical molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) energy calculations. The model systems include an 11-residue peptide, X 2 A 7 O 2 (XAO), where X, A, and O denote diaminobutyric acid, alanine, and ornithine, respectively, and a 9-mer (Arg-Pro-Pro-Gly-Phe-Ser-Ala-Phe-Lys). Spectroscopic and MD data present conflicting evidence regarding the structure of XAO in water; some results indicate that XAO adopts a polyproline II (P II ) conformation, whereas other findings suggest that XAO explores a range of conformations. To investigate this contradiction, we present here the results of MD simulations of XAO and the 9-mer in aqueous solution, combined with QM/MM energy calculations. Full article
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Open AccessArticle Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes
Molecules 2018, 23(9), 2170; https://doi.org/10.3390/molecules23092170
Received: 24 July 2018 / Revised: 23 August 2018 / Accepted: 24 August 2018 / Published: 28 August 2018
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Abstract
In combined quantum-mechanical/molecular-mechanical (QM/MM) dynamics simulations, the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth manner. This yields a mobile QM subsystem with contents that are continuously updated as needed. Here, we tailor the Hamiltonian adaptive many-body correction
[...] Read more.
In combined quantum-mechanical/molecular-mechanical (QM/MM) dynamics simulations, the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth manner. This yields a mobile QM subsystem with contents that are continuously updated as needed. Here, we tailor the Hamiltonian adaptive many-body correction (HAMBC) proposed by Boreboom et al. [J. Chem. Theory Comput. 2016, 12, 3441] to the permuted AP (PAP) scheme. The treatments lead to the HAMBC-PAP method (HPAP), which both conserves energy and produces accurate solvation structures in the test of “water-in-water” model system. Full article
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Open AccessArticle Improvement of Performance, Stability and Continuity by Modified Size-Consistent Multipartitioning Quantum Mechanical/Molecular Mechanical Method
Molecules 2018, 23(8), 1882; https://doi.org/10.3390/molecules23081882
Received: 4 July 2018 / Revised: 25 July 2018 / Accepted: 25 July 2018 / Published: 27 July 2018
Cited by 1 | PDF Full-text (2501 KB) | HTML Full-text | XML Full-text
Abstract
For condensed systems, the incorporation of quantum chemical solvent effects into molecular dynamics simulations has been a major concern. To this end, quantum mechanical/molecular mechanical (QM/MM) techniques are popular and powerful options to treat gigantic systems. However, they cannot be directly applied because
[...] Read more.
For condensed systems, the incorporation of quantum chemical solvent effects into molecular dynamics simulations has been a major concern. To this end, quantum mechanical/molecular mechanical (QM/MM) techniques are popular and powerful options to treat gigantic systems. However, they cannot be directly applied because of temporal and spatial discontinuity problems. To overcome these problems, in a previous study, we proposed a corrective QM/MM method, size-consistent multipartitioning (SCMP) QM/MM and successfully demonstrated that, using SCMP, it is possible to perform stable molecular dynamics simulations by effectively taking into account solvent quantum chemical effects. The SCMP method is characterized by two original features: size-consistency of a QM region among all QM/MM partitioning and partitioning update. However, in our previous study, the performance was not fully elicited compared to the theoretical upper bound and the optimal partitioning update protocol and parameters were not fully verified. To elicit the potential performance, in the present study, we simplified the theoretical framework and modified the partitioning protocol. Full article
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Open AccessArticle Orientation of Laurdan in Phospholipid Bilayers Influences Its Fluorescence: Quantum Mechanics and Classical Molecular Dynamics Study
Molecules 2018, 23(7), 1707; https://doi.org/10.3390/molecules23071707
Received: 4 June 2018 / Revised: 9 July 2018 / Accepted: 12 July 2018 / Published: 13 July 2018
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Abstract
Fluidity of lipid membranes is known to play an important role in the functioning of living organisms. The fluorescent probe Laurdan embedded in a lipid membrane is typically used to assess the fluidity state of lipid bilayers by utilizing the sensitivity of Laurdan
[...] Read more.
Fluidity of lipid membranes is known to play an important role in the functioning of living organisms. The fluorescent probe Laurdan embedded in a lipid membrane is typically used to assess the fluidity state of lipid bilayers by utilizing the sensitivity of Laurdan emission to the properties of its lipid environment. In particular, Laurdan fluorescence is sensitive to gel vs liquid–crystalline phases of lipids, which is demonstrated in different emission of the dye in these two phases. Still, the exact mechanism of the environment effects on Laurdan emission is not understood. Herein, we utilize dipalmitoylphosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC) lipid bilayers, which at room temperature represent gel and liquid–crystalline phases, respectively. We simulate absorption and emission spectra of Laurdan in both DOPC and DPPC bilayers with quantum chemical and classical molecular dynamics methods. We demonstrate that Laurdan is incorporated in heterogeneous fashion in both DOPC and DPPC bilayers, and that its fluorescence depends on the details of this embedding. Full article
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Open AccessArticle Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms
Molecules 2018, 23(6), 1309; https://doi.org/10.3390/molecules23061309
Received: 25 April 2018 / Revised: 22 May 2018 / Accepted: 27 May 2018 / Published: 30 May 2018
PDF Full-text (794 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Combined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM−MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut
[...] Read more.
Combined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM−MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM−MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM−MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme. Full article
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