Energies, structures, and electronic properties of molecules in solution with the C‐PCM solvation model

Cossi, Maurizio; Rega, Nadia; Scalmani, Giovanni; Barone, Vincenzo

doi:10.1002/jcc.10189

Cited by 7,107 publications

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“…Model (CPCM) [35][36][37][38][39] in conjunction with the united atom (UA) cavity-model in-tagged with Kohn-Sham (KS) radii (UAKS) [40][41] with water as a solvent ( = 78.39). We performed frequency calculations by determining analytically the second derivatives of the UB3LYP potential energy surfaces with respect to the fixed atomic nuclear coordinates to determine whether each of the minimized structures corresponded to an energy minimum or a saddle point.…”

Section: Methodsmentioning

confidence: 99%

A Density Functional Theory- and Atoms in Molecules-based Study of NiNTA and NiNTPA Complexes toward Physical Properties Controlling their Stability. A New Method of Computing a Formation Constant

Cukrowski

Govender

2010

Inorg. Chem.

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The log K 1 value of analytical quality was obtained for the NiNTPA complex using the DFTcomputed (at the B3LYP/6-311++G(d,p) level of theory in solvent, CPCM/UAKS) G (aq) values of the lowest energy conformers of the ligands, NTA (nitrilotriacetic acid) and NTPA (nitrilotri-3-propanoic acid), and Ni(II) complexes (NiNTA and NiNTPA). The described mathematical protocol is of general nature. The topological analysis, based on the Quantum Theory of Atoms in Molecules (QTAIM) of Bader, was used to characterize coordination bonds, chelating rings and additional intramolecular interactions in the complexes. The topological data, but not the structural analysis, explained the observed difference in stability of the NiNTA and NiNTPA complexes. It was found that the structural H···H contacts (classically regarded H-clashes, a steric hindrance destabilizing the complex) are in fact the H-H bonds contributing to the overall stability of NiNTPA. Also a CH-O bond was found in NiNTPA. The absence of intramolecular bonds between the atoms that fulfill a distance criterion in NiNTPA is explained by the formation of adjacent intramolecular rings that have larger electron density at the ring critical points when compared with the rings containing these atoms. It is postulated that the strength of a chelating ring (a chelating effect) can be measured by the electron density at the ring critical point. It was found that the strain energy, E s , in the as-in-complex NTPA ligand (E s is significantly lowered by the presence of the intramolecular bonded interactions found by QTAIM) is responsible for the decrease in strength of NiNTPA; the E s ratio (NTPA/NTA) of 1.9 correlates well with the experimental log K 1 ratio (NTA/NTPA) of 1.98.2

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Section: Methodsmentioning

confidence: 99%

A Density Functional Theory- and Atoms in Molecules-based Study of NiNTA and NiNTPA Complexes toward Physical Properties Controlling their Stability. A New Method of Computing a Formation Constant

Cukrowski

Govender

2010

Inorg. Chem.

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“…The conductor-like polarizable continuum model method (CPCM) [41][42][43] with water as solvent was used to take into account the solvent effect. The nature of all stationary points was confirmed by normalmode analysis.…”

Section: Computational Detailsmentioning

confidence: 99%

Photo-Induced Pyridine Substitution in cis-[Ru(bpy)₂(py)₂]Cl₂: A Snapshot by Time-Resolved X-ray Solution Scattering

et al. 2010

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. (2010). Photo-induced pyridine substitution in cis-[Ru(bpy)(2)(py)(2)]Cl-2: a snapshot by time-resolved X-ray solution scattering. Inorganic Chemistry, 49(23), pp. 11240-11248. Permanent WRAP url: http://wrap.warwick.ac.uk/4680 Copyright and reuse:The Warwick Research Archive Portal (WRAP) makes the work of researchers of the University of Warwick available open access under the following conditions. Copyright © and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable the material made available in WRAP has been checked for eligibility before being made available.Copies of full items can be used for personal research or study, educational, or not-forprofit purposes without prior permission or charge. Provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. Publisher's statement:This document is the Accepted Manuscript version of a Published Work that appeared in final form in Inorganic Chemistry, © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/ic102021k A note on versions: The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher's version. Please see the 'permanent WRAP url' above for details on accessing the published version and note that access may require a subscription.

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“…[76,77] We used a dielectric constant of ε = 4 to simulate the polarity of a typical enzymatic environment, and the shape of the cavity was determined by the United Atom Topological Model. [78] 2.6 Graphical representation All molecular representations were created using the UCSF Chimera package.…”

Section: Dft Calculationsmentioning

confidence: 99%

Computational design of a lipase for catalysis of the Diels-Alder reaction

et al. 2010

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Combined molecular docking, molecular dynamics (MD) and density functional theory (DFT) studies have been employed to study catalysis of the Diels-Alder reaction by a modified lipase. Six variants of the versatile enzyme {\em Candida Antarctica} lipase B (CALB) have been rationally engineered {\em in silico} based on the specific characteristics of the pericyclic addition. A kinetic analysis reveals that hydrogen bond stabilization of the transition state and substrate binding are key components of the catalytic process. In the case of substrate binding, which has the greater potential for optimization, both binding strength and positioning of the substrates are important for catalytic efficiency. The binding strength is determined by hydrophobic interactions and can be tuned by careful selection of solvent and substrates. The MD simulations show that substrate positioning is sensitive to cavity shape and size, and can be controlled by a few rational mutations. The well-documented S105A mutation is essential to enable sufficient space in the vicinity of the oxyanion hole. Moreover, bulky residues on the edge of the active site hinders the formation of a sandwich-like near-attack conformer (NAC), and the I189A mutation is needed to obtain enough space above the face of the $\alpha$,$\beta$-double bond on the dienophile. The double mutant S105A/I189A performs quite well for two of three dienophiles. Based on binding constants and NAC energies obtained from MD simulations combined with activation energies from DFT computations, relative catalytic rates ($v_{cat}/v_{uncat}$) of up to $10^3$ are predicted.Response to Reviewers: We are happy with the favorable comments by the reviewers. We have have corrected the manuscript as suggested by reviewer 1 1. A sentence explaining catalytic promiscuity has been added. 2. A paragraph discussing the relationship between the NAC concept and the Reaction Force has been added.We have shortened the manuscript as suggested by reviewer 2. In particular, we have moved information regarding the structural relaxation of protein structure in MD simulations to the supplementary material. Abstract Combined molecular docking, molecular dynamics (MD) and density functional theory (DFT) studies have been employed to study catalysis of the DielsAlder reaction by a modified lipase. Six variants of the versatile enzyme Candida Antarctica lipase B (CALB) have been rationally engineered in silico based on the specific characteristics of the pericyclic addition. A kinetic analysis reveals that hydrogen bond stabilization of the transition state and substrate binding are key components of the catalytic process. In the case of substrate binding, which has the greater potential for optimization, both binding strength and positioning of the substrates are important for catalytic efficiency. The binding strength is determined by hydrophobic interactions and can be tuned by careful selection of solvent and substrates. The MD simulations show that substrate positioning is sensitive to cavity s...

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Energies, structures, and electronic properties of molecules in solution with the C‐PCM solvation model

Cited by 7,107 publications

References 59 publications

A Density Functional Theory- and Atoms in Molecules-based Study of NiNTA and NiNTPA Complexes toward Physical Properties Controlling their Stability. A New Method of Computing a Formation Constant

A Density Functional Theory- and Atoms in Molecules-based Study of NiNTA and NiNTPA Complexes toward Physical Properties Controlling their Stability. A New Method of Computing a Formation Constant

Photo-Induced Pyridine Substitution in cis-[Ru(bpy)₂(py)₂]Cl₂: A Snapshot by Time-Resolved X-ray Solution Scattering

Computational design of a lipase for catalysis of the Diels-Alder reaction

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Energies, structures, and electronic properties of molecules in solution with the C‐PCM solvation model

Cited by 7,107 publications

References 59 publications

A Density Functional Theory- and Atoms in Molecules-based Study of NiNTA and NiNTPA Complexes toward Physical Properties Controlling their Stability. A New Method of Computing a Formation Constant

A Density Functional Theory- and Atoms in Molecules-based Study of NiNTA and NiNTPA Complexes toward Physical Properties Controlling their Stability. A New Method of Computing a Formation Constant

Photo-Induced Pyridine Substitution in cis-[Ru(bpy)2(py)2]Cl2: A Snapshot by Time-Resolved X-ray Solution Scattering

Computational design of a lipase for catalysis of the Diels-Alder reaction

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Product

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Photo-Induced Pyridine Substitution in cis-[Ru(bpy)₂(py)₂]Cl₂: A Snapshot by Time-Resolved X-ray Solution Scattering