Molecules-in-Molecules: An Extrapolated Fragment-Based Approach for Accurate Calculations on Large Molecules and Materials

Mayhall, Nicholas J.; Raghavachari, Krishnan

doi:10.1021/ct200033b

Cited by 201 publications

(279 citation statements)

References 108 publications

Supporting

Mentioning

278

Contrasting

Unclassified

Order By: Relevance

“…The approach was extremely efficient because the demanding CCSD(T)-R12 computations only had to be performed on individual fragments (i.e., HF monomers) and pairs of fragments (i.e., HF dimers). Many hybrid methods are available today that adopt a similar approach by applying two or more levels of theory to the many-body expansion, including extended ONIOM (XO), 223 the molecules in molecules method, 224,225 the hybrid many-body interaction method, 226, 227 the multilevel fragment-based approach, 228 the stratified approximation many-body approach, 229 and the Nbody:Many-body QM:QM technique developed by our group. [230][231][232][233][234][235][236] Ref 237 presents a general framework for and a very lucid overview of the various fragmentation procedures based on the many-body expansion.…”

Section: Strategies For Extending High-accuracy Methods To Larger Clumentioning

confidence: 99%

Wavefunction methods for the accurate characterization of water clusters

Howard

Tschumper

2013

WIREs Comput Mol Sci

View full text Add to dashboard Cite

Although the first ab initio Hartree-Fock computations of the water dimer were reported more than four decades ago, the detailed characterization of water clusters with sophisticated electronic structure techniques remains an important and vibrant area of research. The field of computational quantum chemistry has made significant advances since those pioneering studies. Geometry optimizations of the water dimer can now be carried out at the CCSDTQ level, and CCSD(T) energies can be computed with the aug-cc-pVTZ basis for clusters as large as (H 2 O) 17 . Some of these high-level studies are starting to reveal that the electronic structure is harder to describe for some hydrogen bonds than others. For example, discrepancies between MP2 and CCSD(T) energetics tend to increase when there are qualitative differences in the hydrogen-bonding networks of the water clusters being studied. This review highlights the recent and exciting work in this area and provides an overview of popular strategies for generating reliable properties and benchmark quality energetics for water clusters with correlated wavefunction methods. C 2013 John Wiley & Sons, Ltd.

show abstract

Section: Strategies For Extending High-accuracy Methods To Larger Clumentioning

confidence: 99%

Wavefunction methods for the accurate characterization of water clusters

Howard

Tschumper

2013

WIREs Comput Mol Sci

View full text Add to dashboard Cite

show abstract

“…Other methods, such as the electrostatically embedded pairwise additive model, [13] the binary interaction method, [16] the generalized energy-based fragmentation (GEBF) method, [17] and the electrostatic fieldadapted (EFA) MFCC method [18] rely on point charges to account for global many-body effects. A fragmentation method may also involve several layers of QM methods, [19] for example, a combination of CCSD(T) and MP2. [20] The polarizable multipole interactions with supermolecular pairs (PMISP) method [21] was introduced to address the manybody effects in a simple, yet accurate way, through the use of classical expressions for the interactions between multipoles and polarizabilities.…”

Section: Introductionmentioning

confidence: 99%

Coupled‐Cluster Interaction Energies for 200‐Atom Host–Guest Systems

Andrejić¹,

Ryde²,

Mata³

et al. 2014

ChemPhysChem

View full text Add to dashboard Cite

We have developed a method to calculate interaction energies of large systems (such as host-guest or even protein-ligand systems) at the local coupled-cluster with singles, doubles, and perturbative triples level, and with extrapolation to the limit of a complete basis set. The method is based on the polarizable multipole interactions with supermolecular pairs molecular fractionation approach, which combines a pairwise quantum-mechanical evaluation of the short-range interactions with a polarizable multipole treatment of many-body effects. The method is tested for nine guest molecules binding to an octa-acid host (in total 198-207 atoms), as part of the SAMPL4 blind challenge. From the test calculations, the accuracy of the approach is found to be 10 kJ mol(-1) or better. Comparison with dispersion-corrected density functional theory reveals that the latter underestimates the dispersion contribution for this type of system, which leads to a difference in the ranking of the ligands.

show abstract

“…Molecular tailoring approach (MTA) 32 , molecular fractionation by conjugate capping (MFCC) 26 , fragment molecular orbitals (FMO) 33 , and molecule in molecule 34 are some examples of the divide and conquer approaches that have been extremely successful. MFCC-like approaches have also been developed for hybrid QM/EFP very recently 35 .…”

Section: Complex Biological Systemsmentioning

confidence: 99%

Multiscale Modelling:Hybrid Quantum Mechanics/Molecular Mechanics as an Example and some Recent Developments

Ghosh

2017

Current Science

View full text Add to dashboard Cite

Most of the physical phenomena are multiscale in nature and therefore, to depict it properly one requires multiscale modelling techniques, i.e. physical models that are accurate over multiple length and time scales. The seminal work by Warshel and Levitt marks the beginning of hybrid quantum mechanics/molecular mechanics (QM/MM) method as a successful strategy towards the understanding of chemistry and physics in condensed phases and especially in biological systems. Recently, these methods have been extended to problems such as light-matter interaction, where the QM sub-system is excited from the ground to the excited states. The MM environment provides a field that changes the potential energy landscape of both the ground and excited states in a distinctly different way. In this review, we discuss the general strategy of multiscale modelling with emphasis on hybrid QM/MM and the recent developments in excited state QM/MM methods.Keywords: Biological systems, hybrid quantum mechanics/molecular mechanics, multiscale. Multiscale modellingMANY real-world phenomena are multiscale in nature, i.e. they show complex behaviour that spans over a large range of length and time scales. Length scales can span from few Å in case of bond lengths to a few microns in case of living cell. On the other hand, time scales can range from femtosecond (10 -15 s) for bond vibrations to milliseconds (10 -3 s) for protein folding. In most cases, the different scales (microscopic and macroscopic when it is the length scales) might be a continuum of varying scales. The microscopic behaviour in most cases is specific and complex, while the macroscopic behaviour can be defined by more general rules. For example, the flow of traffic or pedestrians in a crowded street. If one tracks the trajectory of individual pedestrians, they have a specific destination and, therefore, they move towards that destination while avoiding the nearest neighbour interactions or collisions. However, when one zooms out and looks at the average pattern of flow it is very similar to fluid dynamics through a constrained space.Traditionally models have been developed that describe the physics associated with a single time and length scale. However, since the real-world phenomena requires one to span over more than one scale, simulation or modelling techniques have evolved such that they can handle multiple scales in a seamless fashion 1 . Analytical multiscale methodsAnalytical multiscale approaches have been developed for quite a few decades now. In this approach, one derives the rules (or phenomenological models) of a macroscale system from that of a microscale model. Renormalization group (RG) is a classic example of such analytical multiscale method 2 . RG has been used to study phase transitions and critical phenomena. The need for renormalization arises when there are two or more different scales (time or length) and there is no clear demarcation between them. RG is a technique to reduce the degrees of freedom by integrating out less important degrees of freedom...

show abstract

Molecules-in-Molecules: An Extrapolated Fragment-Based Approach for Accurate Calculations on Large Molecules and Materials

Cited by 201 publications

References 108 publications

Wavefunction methods for the accurate characterization of water clusters

Wavefunction methods for the accurate characterization of water clusters

Coupled‐Cluster Interaction Energies for 200‐Atom Host–Guest Systems

Multiscale Modelling:Hybrid Quantum Mechanics/Molecular Mechanics as an Example and some Recent Developments

Contact Info

Product

Resources

About