Hydrogen Bonding and Related Properties in Liquid Water: A Car–Parrinello Molecular Dynamics Simulation Study

Guàrdia, E.; Skarmoutsos, Ioannis; Masia, Marco

doi:10.1021/jp507196q

Cited by 75 publications

(89 citation statements)

References 83 publications

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“…In the present case, the positions of the peaks fall between 100 to 200 cm −10 below the experimental frequencies, consistently with previous Car-Parrinello simulations of H 2 O [51,52].…”

Section: Bulk Phase Propertiessupporting

confidence: 93%

“…Its shape does not seem to be converged, probably because insufficient sampling: note that in this case the RDF is built from a single water molecule out of 64. Various studies of liquid water using the Car-Parrinello method with GGA functionals and an electronic mass comparable to the one employed here, have found overstructured oxygen-oxygen RDFs at room temperature and pressure [42,52,55,56], suggesting that in these conditions this approach represents bulk water in a glassy or supercooled state. Data from one of these works is depicted in Figure 4.…”

Section: Bulk Phase Propertiesmentioning

confidence: 76%

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A quantum-mechanics molecular-mechanics scheme for extended systems

Hunt¹,

Sánchez²,

Scherlis³

2016

J. Phys.: Condens. Matter

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We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car-Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions.With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO 2 anatase (101) solid-liquid interface. This investigation suggests that the inclusion of a second monolayer of H 2 O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces.

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Section: Bulk Phase Propertiessupporting

confidence: 93%

Section: Bulk Phase Propertiesmentioning

confidence: 76%

A quantum-mechanics molecular-mechanics scheme for extended systems

Hunt¹,

Sánchez²,

Scherlis³

2016

J. Phys.: Condens. Matter

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“…Interestingly, some members of the design output ensemble do not contain the hydrogen bond between Histidine 341 and Threonine P -2 , consistent with observations of hydrogen bond breaking and reformation from experimental 81 and MD simulation [82][83][84][85] studies. Indeed, solution NMR studies of ubiquitin showed that threonine residues occupy multiple rotameric states.…”

Section: With 6ov7 To Determinesupporting

confidence: 78%

Computational Analysis of Energy Landscapes Reveals Dynamic Features that Contribute to Binding of Inhibitors to CFTR-Associated Ligand

Holt

Jou²,

Gill

et al. 2019

Preprint

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PDZ domains are small protein-binding domains that interact with short, mostly C-terminal peptides and play important roles in cellular signaling and the trafficking and localization of ion channels. The CFTR-associated ligand PDZ domain (CALP) binds to the cystic fibrosis transmembrane conductance regulator (CFTR) and mediates degradation of mature CFTR through lysosomal pathways. Inhibition of the CALP:CFTR interaction has been explored as a potential therapeutic avenue for cystic fibrosis (CF). 1 Previously, we reported 2 the ensemblebased computational design of a novel 6-residue peptide inhibitor of CALP, which resulted in the most binding-efficient inhibitor of CALP to date. This inhibitor, kCAL01, was designed using OSPREY 3 and displayed significant biological activity in in vitro cell-based assays. Here, we report a crystal structure of kCAL01 bound to CALP (PDB ID: 6OV7). To elucidate the structural basis for the enhanced binding efficiency of kCAL01, we compare this structure to that of a previously developed inhibitor of CALP, iCAL36 (PDB ID: 4E34). In addition to performing traditional structural analysis, we compute the side-chain energy landscapes for each structure using the recently developed MARK * partition function approximation algorithm. 4Analysis of these energy landscapes not only enables approximation of binding thermodynamics for these structural models of CALP:inhibitor binding, but also foregrounds important structural features and reveals dynamic features, both of which contribute to the comparatively efficient binding of kCAL01. The investigation of energy landscapes complements traditional analysis of the few low-energy conformations found in crystal structures, and provides information about the entire conformational ensemble that is accessible to a protein structure model. Finally, we compare the previously reported NMR-based design model ensemble for kCAL01 vs. the new crystal structure and show that, despite the notable differences between the CALP NMR model and crystal structure, many significant features are successfully captured in the design ensemble. This suggests not only that ensemble-based design captured thermodynamically significant features observed in vitro, but also that a design algorithm eschewing ensembles would likely miss the kCAL01 sequence entirely. 2Interactions between proteins and short linear motif peptides are important in many cellular contexts. 5 One such class of peptide-binding proteins is the PDZ (PSD-95, discs large, ZO-1) domain family, characterized by an 80-90 residue motif 6 that adopts a conserved fold comprised of 2-3 α-helices and 5-6 β-strands and binds C-terminal peptides through β-sheet interactions. 7 These domains commonly modulate protein localization and complex assembly 8-10 and regulate cell signalling, 11,12 thereby playing critical roles in auditory and visual systems; 13,14 epilepsy, pain, and addiction; 10,15 synapse formation; 9 cancer; 11,12,16,17 and cystic fibrosis. [18][19][20][21] Protein-peptide interactions have been imp...

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“…We show that our method, which we call "monomer PIMD", correctly captures changes in the structure of water found in a full PIMD simulation but at much lower computational cost.There is great interest in being able to accurately simulate liquid water at the quantum mechanical level. [1][2][3][4] The most widely used methodology for this is density functional theory. However, many density functionals fail to accurately reproduce all of the key properties of water such as its density, compressibility, and diffusion constant.…”

mentioning

confidence: 99%

Using a monomer potential energy surface to perform approximate path integral molecular dynamics simulation of ab initio water at near-zero added cost

Elton

Fritz

Fernández-Serra

2019

Phys. Chem. Chem. Phys.

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It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics simulation of water. The standard way of treating nuclear quantum effects, path integral molecular dynamics (PIMD), multiplies the number of energy/force calculations by the number of beads required. In this work we introduce a method whereby PIMD can be incorporated into a DFT simulation with little extra cost and little loss in accuracy. The method is based on the many body expansion of the energy and has the benefit of including a monomer level correction to the DFT energy. Our method calculates intramolecular forces using the highly accurate monomer potential energy surface developed by Partridge-Schwenke, which is cheap to evaluate. Intermolecular forces and energies are calculated with DFT only once per timestep using the centroid positions. We show how our method may be used in conjunction with a multiple time step algorithm for an additional speedup and how it relates to ring polymer contraction and other schemes that have been introduced recently to speed up PIMD simulations. We show that our method, which we call "monomer PIMD", correctly captures changes in the structure of water found in a full PIMD simulation but at much lower computational cost.There is great interest in being able to accurately simulate liquid water at the quantum mechanical level. [1][2][3][4] The most widely used methodology for this is density functional theory. However, many density functionals fail to accurately reproduce all of the key properties of water such as its density, compressibility, and diffusion constant. Moreover, different density functionals fail in different ways. For instance, PBE creates a overstructured liquid, while many van der Waals (vdW) functionals create an understructured liquid. 5,6 There are nonetheless new meta-GGA functionals such as SCAN 7 or empirically optimized hybrid functionals such as B97M-rV 8 which are producing promising results for liquid water.Most ab initio techniques are based on the Born-Oppenheimer approximation and the assumption that nuclear dynamics can be treated classically. However, over the past two decades a wide range of studies have demonstrated that this is not a good assumption for water because the OH stretching mode of water is very quantum mechanical (zero point temperature T z = ω/2k b = 2600 K), and hydrogen nuclei are delocalized, leading to a large number of nonnegligible nuclear quantum effects (NQEs) -for a recent review, see Ceriotti, et al. 9 In the primary isotope effect, the OH distance is observed to be longer than the OD distance. In the secondary isotope effect, also called the Ubbelöhde effect, the H-bond donoracceptor (oxygen-oxygen) distance R changes upon isotopic substitution. The magnitude and direction of the change depends on the strength of the hydrogen bond, due to competing a) Electronic quantum effects. [10...

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Hydrogen Bonding and Related Properties in Liquid Water: A Car–Parrinello Molecular Dynamics Simulation Study

Cited by 75 publications

References 83 publications

A quantum-mechanics molecular-mechanics scheme for extended systems

A quantum-mechanics molecular-mechanics scheme for extended systems

Computational Analysis of Energy Landscapes Reveals Dynamic Features that Contribute to Binding of Inhibitors to CFTR-Associated Ligand

Using a monomer potential energy surface to perform approximate path integral molecular dynamics simulation of ab initio water at near-zero added cost

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