A Self-consistent Reaction Field Model of Solvation Using Distributed Multipoles. II: Second Energy Derivatives and Application to Vibrational Spectra

Rinaldi, Daniel; Bouchy, A.; Rivail, Jean‐Louis

doi:10.1007/s00214-006-0112-6

Cited by 22 publications

(21 citation statements)

References 18 publications

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“…It is known that the PCM model tends to overestimate the solvent effect at least regarding the changes in molecular vibrations. 20 Accordingly, we propose that the values in Ref. 13 are overestimated and apply a scaling factor of 0.75.…”

Section: -3mentioning

confidence: 99%

Spectroscopic study of cis-to-trans tunneling reaction of HCOOD in rare gas matrices

Domanskaya¹,

Marushkevich²,

Khriachtchev³

et al. 2009

The Journal of Chemical Physics

106

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The higher energy conformer (cis) of HCOOD is prepared by vibrational excitation of the trans form. The cis conformer decays back to the conformational ground state (trans) via tunneling of deuterium. The tunneling process in HCOOD in rare gas matrices is extremely slow (in scale of weeks). We present new measurements of the tunneling rate constants, which characterize the efficiency of the cis-to-trans conversion process in Ne, Ar, Kr, and Xe matrices. The tunneling rates of HCOOD follow the trend k(Xe) approximately = k(Kr)>k(Ar) approximately = k(Ne), which is anomalous with respect to the reaction barrier of the solvated molecule. We propose a semiempirical energetic scheme of solid state solvation, which is consistent with all experimental observation. The temperature dependence of the tunneling constants rates of HCOOD is very weak compared to HCOOH in all matrices. The fundamental vibrational frequencies of the cis and trans conformers of HCOOD in various matrices are reported.

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Section: -3mentioning

confidence: 99%

Spectroscopic study of cis-to-trans tunneling reaction of HCOOD in rare gas matrices

Domanskaya¹,

Marushkevich²,

Khriachtchev³

et al. 2009

The Journal of Chemical Physics

106

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“…22,23 We will briefly restate the results of Im et al to introduce the approach extended here for use with the PMPB model. 20 The solvation free energy Δ G of a permanent charge distribution is (13) where q is a column vector of fractional charges, is the transpose of a column vector containing the electrostatic potential of the solvated system and is the corresponding vacuum potential. The number of components in each vector is equal to the number of grid points used to represent the system.…”

Section: B Lpbe Energies and Gradients For Fixed Partial Charge Forcmentioning

confidence: 99%

“…2,9 In spite of the fact that the dipole moment of a polar solute can increase by 30% or more during transfer from gas to aqueous phase, empirical potentials have typically neglected explicit treatment of polarization for reasons of computational efficiency. However, ab initio implicit solvent models, including the Polarizable Continuum Model (PCM) introduced in 1981 by Miertus, Scrocco and Tomasi 10,11 , the Conductor-Like Screening Model (COSMO) of Klamt 12 , the distributed multipole approach of Rinaldi et al 13 and the SMx series of models introduced in the early 90s by Cramer and Truhlar 14 have long incorporated self-consistent reaction fields (SCRF). 10,15 These models allow the solute, described using a range of ab initio or semi-empirical levels of theory, and continuum solvent to relax self-consistently based on their mutual interaction.…”

Section: Introductionmentioning

confidence: 99%

Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum

Schnieders

Baker

Ren

et al. 2007

The Journal of Chemical Physics

116

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Modeling the change in the electrostatics of organic molecules upon moving from vacuum into solvent, due to polarization, has long been an interesting problem. In vacuum, experimental values for the dipole moments and polarizabilities of small, rigid molecules are known to high accuracy; however, it has generally been difficult to determine these quantities for a polar molecule in water. A theoretical approach introduced by Onsager used vacuum properties of small molecules, including polarizability, dipole moment and size, to predict experimentally known permittivities of neat liquids via the Poisson equation. Since this important advance in understanding the condensed phase, a large number of computational methods have been developed to study solutes embedded in a continuum via numerical solutions to the Poisson-Boltzmann equation (PBE). Only recently have the classical force fields used for studying biomolecules begun to include explicit polarization in their functional forms. Here we describe the theory underlying a newly developed Polarizable Multipole PoissonBoltzmann (PMPB) continuum electrostatics model, which builds on the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. As an application of the PMPB methodology, results are presented for several small folded proteins studied by molecular dynamics in explicit water as well as embedded in the PMPB continuum. The dipole moment of each protein increased on average by a factor of 1.27 in explicit water and 1.26 in continuum solvent. The essentially identical electrostatic response in both models suggests that PMPB electrostatics offers an efficient alternative to sampling explicit solvent molecules for a variety of interesting applications, including binding energies, conformational analysis, and pK a prediction. Introduction of 150 mM salt lowered the electrostatic solvation energy between 2-13 kcal/mole, depending on the formal charge of the protein, but had only a small influence on dipole moments.

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“…Compared with calculations in weaker dielectrical surrounding (see Table I, Supplementary Material), the NCM–PCM electrostatic energies difference is inferior to 0.20 kcal · mol −1 in average [from α: 1.0 to 3.0] suggesting that both models are equivalent when identical solute cavity sizes are used. Moreover, D. Rinaldi et al 21 show that for a identical solute cavity volume, the equivalence NCM–PCM remains useful for reasonable dielectrical surroundings, i.e., the solvent used is acetonitrile (ϵ r of 36.6).…”

Section: Resultsmentioning

confidence: 99%

“…It is important to underline that only the electrostatic term is needed to get the wave function of the solute (nonelectrostatic contributions are considered as a corrective post‐treatment of the model). In NCM formalism 16–21, the Coulomb solute–solvent interactions energy is evaluated via a multicentric multipolar Taylor expansion of the electrostatic potential. This potential is called reaction potential, giving rise to a reaction field.…”

Section: Methodsmentioning

confidence: 99%

Early fetal development of the intermediate tendon of the human digastricus and omohyoideus muscles: A critical difference in histogenesis

et al. 2011

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The digastricus and omohyoideus muscles are known to carry two muscle bellies connected by an intermediate tendon. However, according to our histological observations of 22 fetuses (7-20 weeks of gestation), the mode of formation of the intermediate tendon was critically different between these two muscles. At 7-9 weeks, the posterior belly of the digastricus carried a definite intramuscular tendon continuous with a long descending tendon. The stylohyoideus, external carotid artery and hypoglossal nerve appeared to impede attachment of the tendon to the Reichert or hyoid cartilage. The digastricus anterior belly did not contain any intramuscular tendon, but desmin-positive muscle fibers consistently surrounded a bulb-like mesenchymal condensation at the caudal free end of the digastricus posterior tendon. Thus, most parts of the digastricus tendon were apparently derived from the posterior belly. In contrast, the omohyoideus always possessed a single long muscle belly until 15 weeks. The intermediate tendon first appeared at 15 weeks as a short plate-like connective structure along the medial margin of the muscle. Vimentin immunoreactivity suggested the presence of mechanical stress along the plate-like tissue, possibly due to bending of the long muscle. Muscle fibers were replaced by collagen fibers to form an intermediate tendon by 20 weeks.

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A Self-consistent Reaction Field Model of Solvation Using Distributed Multipoles. II: Second Energy Derivatives and Application to Vibrational Spectra

Cited by 22 publications

References 18 publications

Spectroscopic study of cis-to-trans tunneling reaction of HCOOD in rare gas matrices

Spectroscopic study of cis-to-trans tunneling reaction of HCOOD in rare gas matrices

Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum

Early fetal development of the intermediate tendon of the human digastricus and omohyoideus muscles: A critical difference in histogenesis

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