Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

Giese, Timothy J.; Chen, Haoyuan; Huang, Ming; York, Darrin M.

doi:10.1021/ct401035t

Cited by 31 publications

(68 citation statements)

References 110 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…12,23 mDC and X-Pol are conceptually equivalent but differ in their details of how the fragments interact with one another. The X-Pol method interacts the fragments using a traditional QM/MM potential; however, this potential depends upon which fragment is considered to be the QM region.…”

Section: Development Of a Qmff Based On The MDC Methodsmentioning

confidence: 99%

Recent Advances toward a General Purpose Linear-Scaling Quantum Force Field

et al. 2014

Self Cite

View full text Add to dashboard Cite

ConspectusThere is need in the molecular simulation community to develop new quantum mechanical (QM) methods that can be routinely applied to the simulation of large molecular systems in complex, heterogeneous condensed phase environments. Although conventional methods, such as the hybrid quantum mechanical/molecular mechanical (QM/MM) method, are adequate for many problems, there remain other applications that demand a fully quantum mechanical approach. QM methods are generally required in applications that involve changes in electronic structure, such as when chemical bond formation or cleavage occurs, when molecules respond to one another through polarization or charge transfer, or when matter interacts with electromagnetic fields. A full QM treatment, rather than QM/MM, is necessary when these features present themselves over a wide spatial range that, in some cases, may span the entire system. Specific examples include the study of catalytic events that involve delocalized changes in chemical bonds, charge transfer, or extensive polarization of the macromolecular environment; drug discovery applications, where the wide range of nonstandard residues and protonation states are challenging to model with purely empirical MM force fields; and the interpretation of spectroscopic observables. Unfortunately, the enormous computational cost of conventional QM methods limit their practical application to small systems. Linear-scaling electronic structure methods (LSQMs) make possible the calculation of large systems but are still too computationally intensive to be applied with the degree of configurational sampling often required to make meaningful comparison with experiment.In this work, we present advances in the development of a quantum mechanical force field (QMFF) suitable for application to biological macromolecules and condensed phase simulations. QMFFs leverage the benefits provided by the LSQM and QM/MM approaches to produce a fully QM method that is able to simultaneously achieve very high accuracy and efficiency. The efficiency of the QMFF is made possible by partitioning the system into fragments and self-consistently solving for the fragment-localized molecular orbitals in the presence of the other fragment’s electron densities. Unlike a LSQM, the QMFF introduces empirical parameters that are tuned to obtain very accurate intermolecular forces. The speed and accuracy of our QMFF is demonstrated through a series of examples ranging from small molecule clusters to condensed phase simulation, and applications to drug docking and protein–protein interactions. In these examples, comparisons are made to conventional molecular mechanical models, semiempirical methods, ab initio Hamiltonians, and a hybrid QM/MM method. The comparisons demonstrate the superior accuracy of our QMFF relative to the other models; nonetheless, we stress that the overarching role of QMFFs is not to supplant these established computational methods for problems where their use is appropriate. The role of QMFFs within the toolbox of mult...

show abstract

Section: Development Of a Qmff Based On The MDC Methodsmentioning

confidence: 99%

Recent Advances toward a General Purpose Linear-Scaling Quantum Force Field

et al. 2014

Self Cite

View full text Add to dashboard Cite

show abstract

“…Consequently, it has been shown that water clusters lose their hydrogen bond angles, instead choosing to adopt TIP3P-like, 133 planar hydrogen bonding motifs. 21,59,61 To correct for this deficiency, the mDC method concocts a new, auxiliary atomic multipole representation of the fragment density that is solely used for the inter-fragment Coulomb interactions.…”

Section: Inter-fragment Coupling Schemesmentioning

confidence: 99%

Quantum mechanical force fields for condensed phase molecular simulations

Giese

York

2017

J. Phys.: Condens. Matter

View full text Add to dashboard Cite

Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model for the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.

show abstract

“…54 This approach has been adopted in the present work. In essence, a second set of atomic charges and higher-order atomic multipoles are chosen to interact with the implicit solvent response, while leaving the DFTB3 solute-solute interactions unchanged from their original form.…”

Section: A Solute Charge Density Interaction Correctionmentioning

confidence: 99%

“…The implicit solvent model response is caused by the electrostatic potential of the solute; therefore, an auxiliary set of atomic multipole moments from the DFTB3 density matrix was constructed using the prescription developed in Ref. 54. The inclusion of these multipole moments leads to the alleviation or complete elimination of these systematic errors, thus informing the decision to abandon parameterization efforts using the conventional DFTB3 monopole approximation.…”

Section: A Vr-scosmo Model Parameterizationmentioning

confidence: 99%

VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions

Kuechler

Giese

York

2016

The Journal of Chemical Physics

Self Cite

View full text Add to dashboard Cite

To better represent the solvation effects observed along reaction pathways, and of ionic species in general, a charge-dependent variable-radii smooth conductor-like screening model (VR-SCOSMO) is developed. This model is implemented and parameterized with a third order density-functional tight binding quantum model, DFTB3/3OB-OPhyd, a quantum method which was developed for organic and biological compounds, utilizing a specific parameterization for phosphate hydrolysis reactions. Unlike most other applications with the DFTB3/3OB model, an auxiliary set of atomic multipoles is constructed from the underlying DFTB3 density matrix which is used to interact the solute with the solvent response surface. The resulting method is variational, produces smooth energies, and has analytic gradients. As a baseline, a conventional SCOSMO model with fixed radii is also parameterized. The SCOSMO and VR-SCOSMO models shown have comparable accuracy in reproducing neutral-molecule absolute solvation free energies; however, the VR-SCOSMO model is shown to reduce the mean unsigned errors (MUEs) of ionic compounds by half (about 2-3 kcal/mol).

show abstract

Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

Cited by 31 publications

References 110 publications

Recent Advances toward a General Purpose Linear-Scaling Quantum Force Field

Recent Advances toward a General Purpose Linear-Scaling Quantum Force Field

Quantum mechanical force fields for condensed phase molecular simulations

VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions

Contact Info

Product

Resources

About