scholarly journals Assessment of the VDW interaction converting DMAPS from the thermal-motion form to the hydrogen-bonded form

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Masae Takahashi ◽  
Hiroshi Matsui ◽  
Yuka Ikemoto ◽  
Makoto Suzuki ◽  
Nobuyuki Morimoto
Keyword(s):  
Dft Calculations ◽  
Density Functional ◽  
Amorphous State ◽  
Polarizable Continuum Model ◽  
Thermal Motion ◽  
Isosbestic Point ◽  
Sensitive Function ◽  
Stimuli Sensitive ◽  
Polarizable Continuum ◽  
Hydrogen Bonded

Abstract Assessment of van der Waals (VDW) interactions is fundamental to all of the central quest of structure that regulates the biological function. VDW interactions contributing to intramolecular weak hydrogen bonding are regarded as an important force to regulate the thermal stimuli-sensitive function of sulfobetaine methacrylate, DMAPS. We present here the conversion from the thermal-motion form at room temperature to the weak-hydrogen-bonded form against thermal motion as a terahertz spectral change with a definite isosbestic point from an absorption peak of one form to the other. Vibrational absorptions are used as a probe for assessing VDW interactions in conjunction with highly reliable and well-established density functional theory (DFT) calculations for analysis. Complicated spectral features and uncertain conformations of DMAPS in the amorphous state are clearly resolved under the polarizable continuum model and the dispersion correction for the pure DFT calculations.

scholarly journals Predicting the UV–vis spectra of oxazine dyes

2011 ◽  
Vol 7 ◽  
pp. 432-441 ◽  
Author(s):  
Scott Fleming ◽  
Andrew Mills ◽  
Tell Tuttle
Keyword(s):  
Excitation Energy ◽  
Density Functional ◽  
Polarizable Continuum Model ◽  
Implicit Solvent ◽  
Continuum Approach ◽  
Excitation Energies ◽  
Functional Theory ◽  
Partial Charges ◽  
Td Dft ◽  
Polarizable Continuum

In the current work we have investigated the ability of time-dependent density functional theory (TD-DFT) to predict the absorption spectra of a series of oxazine dyes and the effect of solvent on the accuracy of these predictions. Based on the results of this study, it is clear that for the series of oxazine dyes an accurate prediction of the excitation energy requires the inclusion of solvent. Implicit solvent included via a polarizable continuum approach was found to be sufficient in reproducing the excitation energies accurately in the majority of cases. Moreover, we found that the SMD solvent model, which is dependent on the full electron density of the solute without partitioning into partial charges, gave more reliable results for our systems relative to the conductor-like polarizable continuum model (CPCM), as implemented in Gaussian 09. In all cases the inclusion of solvent reduces the error in the predicted excitation energy to <0.3 eV and in the majority of cases to <0.1 eV.

scholarly journals Н-комплексы 1,2-нафтохинона с молекулами воды в водном растворе и их влияние на сдвиги полос поглощения

2021 ◽  
Vol 129 (5) ◽  
pp. 599
Author(s):  
С.Н. Цеплина ◽  
E.E. Цеплин
Keyword(s):  
Quantum Chemical ◽  
Continuum Model ◽  
Density Functional ◽  
Water Solution ◽  
Polarizable Continuum Model ◽  
Water Molecules ◽  
Absorption Bands ◽  
Functional Theory ◽  
Polarizable Continuum ◽  
Polar Water

Optical absorption spectra of 1,2-naphthoquinone in non-polar (n-hexane) and polar (water) solvents were obtained. It is shown that the use of quantum chemical calculations based on time-dependent density functional theory (TDDFT B3LYP/6-311+G(d, p)) with the polarizable continuum model (PCM) for calculating 1,2-naphthoquinone in a solution of n-hexane and hydrogen complex of 1,2-naphthoquinone with two water molecules in an aqueous medium describes well the shifts of the absorption bands of 1,2-naphthoquinone in a water solution compared to a solution in n-hexane. Based on the analysis of deviations of the calculated band shifts from the experimental ones, the question of the formation of 1,2-naphthoquinone hydrogen complexes with n water molecules (n = 1-4) in an aqueous solution is considered.

The fragment molecular orbital method combined with density-functional tight-binding and the polarizable continuum model

2016 ◽  
Vol 18 (32) ◽  
pp. 22047-22061 ◽  
Author(s):  
Yoshio Nishimoto ◽  
Dmitri G. Fedorov
Keyword(s):  
Molecular Structure ◽  
Molecular Orbital ◽  
Continuum Model ◽  
Density Functional ◽  
Tight Binding ◽  
Polarizable Continuum Model ◽  
Orbital Method ◽  
Molecular Orbital Method ◽  
Polarizable Continuum ◽  
Structure Of Proteins

The electronic gap in proteins is analyzed in detail, and it is shown that FMO-DFTB/PCM is efficient and accurate in describing the molecular structure of proteins in solution.

DENSITY FUNCTIONAL THEORY STUDY ON THE MECHANISM OF TRIMETHYLAMINE-CATALYZED BAYLIS–HILLMAN REACTION

2010 ◽  
Vol 09 (supp01) ◽  
pp. 65-75 ◽  
Author(s):  
JING LI ◽  
WAN-YI JIANG
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Dft Method ◽  
Polarizable Continuum Model ◽  
Functional Theory ◽  
Reaction Barrier ◽  
Hydrogen Shift ◽  
Rate Determining Step ◽  
The Density Functional Theory ◽  
Polarizable Continuum

The trimethylamine-catalyzed Baylis–Hillman reaction of formaldehyde and vinylaldehyde has been studied with the density functional theory (DFT) method of B3LYP/6-31+G(d,p). In the gas phase, the reaction involves an amine–formaldehyde–vinylaldehyde trimolecular addition transition structure followed by rate-determining intramolecular 1,3-hydrogen shift. When a bulk solvent effect of water was considered with conductor-like polarizable continuum model (CPCM), the reaction was found to follow the sequence of Michael-addition of amine to vinylaldehyde (step 1), addition of formaldehyde (step 2), and 1,3-hydrogen shift (step 3), with the 1,3-hydrogen shift as rate-determining. The overall reaction barrier is significantly reduced. When a molecule of water is involved in the reaction, the 1,3-hydrogen shift is significantly promoted so that the rate-determining step becomes the C–C bond formation. The calculated overall reaction barrier is in agreement with experimental observations.

THEORETICAL STUDY OF GLYCINE CONFORMERS

2008 ◽  
Vol 07 (04) ◽  
pp. 889-909 ◽  
Author(s):  
HONG-WEI KE ◽  
LI RAO ◽  
XIN XU ◽  
YI-JING YAN
Keyword(s):  
Potential Energy Surfaces ◽  
Density Functional ◽  
Polarizable Continuum Model ◽  
Basis Sets ◽  
Dft Methods ◽  
Solvent Interactions ◽  
Solvation Effects ◽  
Moller Plesset ◽  
Energy Surfaces ◽  
Polarizable Continuum

Glycine conformers were investigated with three density functional theory (DFT) methods (B3LYP, PBE1PBE, X3LYP), and the second order Møller–Plesset perturbation theory (MP2) combined with basis sets of 6-31+G*, aug-cc-pVDZ, and aug-cc-pVTZ. Solvation effects were considered by using polarizable continuum model. Results from B3LYP and X3LYP were in generally good agreement with those of MP2, while PBE1PBE was shown to be inferior for the description of conformational potential energy surfaces. Conformers Ip, IIp, IIn, IIIp, IIIn, and IVn were all found to be low-lying states within 2.0 kcal/mol, with Ip being the global minimum in gas phase. Solvation effects can significantly change the nature of the conformational surfaces of glycine. A proper description of conformational equilibrium demands for a good treatment of both long-range and short-range solute–solvent interactions.

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