Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory

Tannor, David J.; Marten, Bryan; Murphy, Ryan O.; Friesner, Richard A.; Sitkoff, Doree; Nicholls, Anthony; Honig, Barry; Ringnalda, Murco N.; Goddard, William A.

doi:10.1021/ja00105a030

Cited by 1,046 publications

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“…At the final geometry, the solvation energy in AN (dielectric constant 35.69, density 0.7857 g/cm 3 at 20°C, 43 probe radius 2.18 Å) is also calculated in B3LYP/ 6-31G** (since the solvation energy is not very sensitive to the choice of basis set 42 ) using the Poisson-Boltzmann continuum-solvation model. 44,45 The following atomic radii are used (in Å): 42 H 1.15, C 1.9, N 1.6, O 1.6, F 1.682, P 2.074, and S 1.7 (which has been changed from 1.9 to reproduce the experimental reduction potentials of TTF). All calculations are done using Jaguar v5.5.…”

Section: Methodsmentioning

confidence: 99%

Mechanism of Oxidative Shuttling for [2]Rotaxane in a Stoddart−Heath Molecular Switch: Density Functional Theory Study with Continuum-Solvation Model

Jang

Goddard

2006

J. Phys. Chem. B

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The central component of the programmable molecular switch demonstrated recently by Stoddart and Heath is [2]rotaxane, which consists of a cyclobis-(paraquat-p-phenylene) ring-shaped shuttle [(CBPQT 4+ )(PF 6 -) 4 ] encircling a finger and moving between two stations on the finger: tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP). We report here a quantum mechanics (QM) study of the mechanism by which movement of the ring (and in turn the on-off switching) is controlled by the oxidation-reduction process. We use B3LYP density functional theory to describe how oxidation of the [2]rotaxane components (in using PoissonBoltzmann continuum-solvation theory for acetonitrile solution) induces the motions associated with switching (translation of the ring). These calculations support the proposal that oxidation occurs on TTF, leading to repulsion between two positive charge centers (TTF 2+ and CBPQT 4+ ) that drives the CBPQT 4+ ring from the TTF 2+ station toward the neutral DNP station. The theory also supports the experimental observation that the first and second oxidation potentials are nearly the same (separated by 0.09 eV in the QM). This excellent agreement between the QM and experiment suggests that QM can be useful in designing new systems.

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Section: Methodsmentioning

confidence: 99%

Mechanism of Oxidative Shuttling for [2]Rotaxane in a Stoddart−Heath Molecular Switch: Density Functional Theory Study with Continuum-Solvation Model

Jang

Goddard

2006

J. Phys. Chem. B

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“…Corrections of 3-4 kcal/mol were calculated for these long-range dispersion interactions. To reproduce the polarization effects of the solvent used in the experiments, the selfconsistent reaction field (SCRF) method implemented in Jaguar 5.5 was employed [27,28]. The solvent was modeled as a macroscopic continuum with a dielectric constant of 36.6 (corresponding to acetonitrile), and the solute was placed in a cavity contained in this continuous medium.…”

Section: Computational Detailsmentioning

confidence: 99%

DFT Study on the Catalytic Reactivity of a Functional Model Complex for Intradiol-Cleaving Dioxygenases

et al. 2010

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The enzymatic ring-cleavage of catechol derivatives is catalyzed by two groups of dioxygenases, extradiol-and intradiol-cleaving dioxygenases. Although having a different oxidation state of their non-heme iron site and a different ligand coordination, both groups of enzymes involve a common peroxy intermediate in their catalytic cycle. The factors that lead to either extradiol cleavage resulting in 2-hydroxymuconaldehyde, or intradiol cleavage resulting in muconic acid, are not fully understood. Well characterized model compounds that mimic the functionality of these enzymes offer a basis for direct comparison to theoretical results. In this study the mechanism of a biomimetic iron complex is investigated with Density Functional Theory (DFT). This complex catalyzes the ring opening of catecholate with exclusive formation of the intradiol cleaved product. Several spin states are possible for the transition metal system, with the quartet state found to be of main importance during the reaction course. The mechanism investigated provides an explanation for the observed selectivity of the complex. First, a bridging peroxide is formed, which decomposes to an alkoxy-radical by O-O homolysis. In contrast to the subsequent barrier-free intradiol C-C bond cleavage, the extradiol pathway proceeds via the formation of an epoxide, which requires an additional activation barrier.

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“…Initially, a combination of in vacuo ab initio quantum chemical and classical solvation energy calculations [73,74] was implemented. Later, various techniques were developed which allow for the self-consistent ab initio treatment of a molecule embedded in a dielectric continuum [75,76,77]. At present, there exist a number of ab initio as well as semi-empirical techniques which try to account for the realistic atomic structure and charge distribution of the environment via explicit incorporation of protein (or solution) point charges in the electronic Hamiltonian of the quantum chemically treated substrate [78,79,80,81,82,83].…”

Section: Quantum Chemistry Of In Situ Retinalmentioning

confidence: 99%

Quantum Chemistry of in situ Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin

Logunov

Schulten

1996

Quantum Mechanical Simulation Methods for Studying Biological Systems

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1A combination of molecular dynamics and quantum chemistry techniques have been employed to study the electronic excitation and conformational potential surface of retinal in the binding site of bacteriorhodopsin (bR). The CASSCF(6,9)/6-31G level of ab initio calculations (within Gaussian92) has been used for the treatment of both the ground (S0) and excited (S1) states of retinal. Charges of all atoms in the protein are represented by spherical Gaussians and explicitly included in the electronic Hamiltonian of retinal. Spectral properties have been analyzed for the native bR pigment as well as for its D85N mutant.The calculated relative shift in the absorption maxima between the two pigments is in better agreement with experiment than the computed absolute parameters of the absorption line shapes. The dark adaptation processes in bacteriorhodopsin (which involves rotation around the 13-14 and the 15-N retinal double bonds) has been modelled by following the pre-defined reaction coordinate. Our simulations support the notion that the isomerization process is catalyzed by the protonation of an aspartic acid (Asp85) side group of bacteriorhodopsin. 2 IntroductionBacteriorhodopsin (bR) spans the cell membrane of Halobacterium halobium and functions as a light-driven proton pump. bR contains seven α-helices which enclose the prosthetic group, all-trans retinal, bound via a protonated Schiff base linkage to Lys-216. Figure 1a shows the chemical structure of retinal and its conventional numbering scheme. The bR structure is presented in Fig. 2a. Retinal absorbs light and undergoes a photoisomerization process; the thermal reversal of this reaction is coupled to transfer of a proton from the cytoplasmic side (top in Fig. 2a) to the extracellular side (bottom in Fig. 2a) of the protein.Recent reviews that discuss the structure and function of bR are [1,2,3,4,5,6,7]. Figure 1 here Bacteriorhodopsin accomplishes its function through a cyclic process initiated by absorption of a photon. This photon triggers an isomerization of retinal, which proceeds then through several intermediate states identified by their absorption spectra. An accepted kinetic scheme for this cycle is an unbranched series of intermediates, shown in Fig. 3. Photoisomerization occurs in the bR 568 → J 625 transition. During the L 550 → M 412 transition the Schiff base proton is transferred to Asp-85 and, subsequently, to the outside of the cell [8,9,10,11,12,13]. During the M 412 → N 520 transition, a proton is transferred to the Schiff base from Asp-96, which then takes up a proton from the cytoplasmic environment [13]. The reaction cycle is completed as the protein returns to bR 568 via the O 640 intermediate. Figure 2 here When bR is allowed to equilibrate in the dark, it converts within an hour to a 2:1 mixture containing 13-cis retinal and all-trans retinal bR [14]. The protein containing the 13-cis retinal isomer of bRis referred to as the dark adapted (DA) pigment of bR, bR 548 , which absorbs at 548 nm. bR 548 contains, actually, retinal in a 1...

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Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory

Cited by 1,046 publications

References 0 publications

Mechanism of Oxidative Shuttling for [2]Rotaxane in a Stoddart−Heath Molecular Switch: Density Functional Theory Study with Continuum-Solvation Model

Mechanism of Oxidative Shuttling for [2]Rotaxane in a Stoddart−Heath Molecular Switch: Density Functional Theory Study with Continuum-Solvation Model

DFT Study on the Catalytic Reactivity of a Functional Model Complex for Intradiol-Cleaving Dioxygenases

Quantum Chemistry of in situ Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin

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