A configuration analysis for fragment interaction

Mochizuki, Yuji; Fukuzawa, Kaori; Kato, Akifumi; Tanaka, Shigenori; Kitaura, Kazuo; Nakano, Tatsuya

doi:10.1016/j.cplett.2005.05.079

Cited by 88 publications

(65 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…However, until very recently, in addition to the total properties of the whole system, only the net pair interaction energies (PIEs) were defined, without any physical structure of their components. Mochizuki et al 30 proposed a configuration analysis for fragment interaction (CAFI) to obtain the polarization and charge transfer contributions to the PIEs; however, as pointed out below, both differ from the conventional definitions.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Pair interaction energy decomposition analysis

2006

Self Cite

View full text Add to dashboard Cite

Abstract:The energy decomposition analysis (EDA) by Kitaura and Morokuma was redeveloped in the framework of the fragment molecular orbital method (FMO). The proposed pair interaction energy decomposition analysis (PIEDA) can treat large molecular clusters and the systems in which fragments are connected by covalent bonds, such as proteins. The interaction energy in PIEDA is divided into the same contributions as in EDA: the electrostatic, exchange-repulsion, and charge transfer energies, to which the correlation (dispersion) term was added. The careful comparison to the ab initio EDA interaction energies for water clusters with 2-16 molecules revealed that PIEDA has the error of at most 1.2 kcal/mol (or about 1%). The analysis was applied to (H 2 O) 1024 , the helix, turn, and strand of polyalanine (ALA) 10 , as well as to the synthetic protein (PDB code 1L2Y) with 20 residues. The comparative aspects of the polypeptide isomer stability are discussed in detail.

show abstract

Section: Introductionmentioning

confidence: 99%

“…30) defines the polarization to be the quantity, which should be denoted as DE PLs in the context of this work. That is, it is the stabilization contribution to the polarization computed for the PL state, which is not equal to DE PL0s .…”

mentioning

confidence: 99%

Pair interaction energy decomposition analysis

2006

Self Cite

View full text Add to dashboard Cite

show abstract

“…69,70 Moreover, they treat both inter-and intramolecular 18,19,43,71 (including through-bond) interactions on equal footing (including through bond) and, thus, capably describe phenomena that are of a mixed or non-covalent nature, e.g., dative bonds, 27,72,73 as well as chemisorption and physisorption processes 221,222 (through a "periodic EDA" by Tonner et al 223 ). Owing to the numerous levels of accuracy possible, including multireference variants, 41,74 it is also possible to treat strongly correlated systems 75 and molecules having elongated bonds.…”

Section: Figmentioning

confidence: 99%

“…3). To separate exchange and electrostatic interactions, KM EDA (as well as some later developed EDAs including CAFI 18 and PIEDA 19 ) uses the wavefunctions that are not fully antisymmetric, which can lead to the overestimation of the induction energy 20 these methods are hindered in describing problems involving steric clashes. However, for non-covalent interactions, the exchange interaction problem becomes less important as it primarily describes interactions that are short-range in nature.…”

Section: Variational Energy Decomposition Analysismentioning

confidence: 99%

Perspective: Found in translation: Quantum chemical tools for grasping non-covalent interactions

Pastorczak¹,

Corminbœuf²

2017

The Journal of Chemical Physics

105

102

View full text Add to dashboard Cite

Today's quantum chemistry methods are extremely powerful but rely upon complex quantities such as the massively multidimensional wavefunction or even the simpler electron density. Consequently, chemical insight and a chemist's intuition are often lost in this complexity leaving the results obtained difficult to rationalize. To handle this overabundance of information, computational chemists have developed tools and methodologies that assist in composing a more intuitive picture that permits better understanding of the intricacies of chemical behavior. In particular, the fundamental comprehension of phenomena governed by non-covalent interactions is not easily achieved in terms of either the total wavefunction or the total electron density, but can be accomplished using more informative quantities. This perspective provides an overview of these tools and methods that have been specifically developed or used to analyze, identify, quantify, and visualize non-covalent interactions. These include the quantitative energy decomposition analysis schemes and the more qualitative class of approaches such as the Non-covalent Interaction index, the Density Overlap Region Indicator, or quantum theory of atoms in molecules. Aside from the enhanced knowledge gained from these schemes, their strengths, limitations, as well as a roadmap for expanding their capabilities are emphasized. ©2017Author(s

show abstract

“…The specific interactions between CAP and cAMP or DNA were investigated more accurately [7] by ab initio fragment MO (FMO) method [8]. However, the FMO calculation was carried out, considering some domains of CAP contributing to the binding between CAP and DNA.…”

Section: Introductionmentioning

confidence: 99%

Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

Matsushita

Murakawa

Shimamura

et al. 2015

AIP Conference Proceedings

View full text Add to dashboard Cite

Abstract. The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

show abstract

A configuration analysis for fragment interaction

Cited by 88 publications

References 30 publications

Pair interaction energy decomposition analysis

Pair interaction energy decomposition analysis

Perspective: Found in translation: Quantum chemical tools for grasping non-covalent interactions

Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

Contact Info

Product

Resources

About