Atom additive model based on dipole field tensor to compute static average molecular dipole polarizabilities

Mkadmh, Ahmed M.; Hinchliffe, Alan; Abu-Awwad, Fakhr M.

doi:10.1016/j.theochem.2008.12.030

Cited by 14 publications

(14 citation statements)

References 32 publications

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“… T ij represents the dipole field tensor which is the induced dipole field exerted on the i th atom by the j th one within the molecule given by the relation T ij = r ij − 3 ( I − 3r ij − 2 r ij r ij ), I is a 3 × 3 unit matrix, r ij r ij is a 3 × 3 tensor resulted from the product of the first radius vector between the i th and the j th atoms with the transpose of the second one with r ij as its scalar magnitude. [ 46,49 ]…”

Section: Resultsmentioning

confidence: 99%

“…r ij r ij ), I is a 3 × 3 unit matrix, r ij r ij is a 3 × 3 tensor resulted from the product of the first radius vector between the ith and the jth atoms with the transpose of the second one with r ij as its scalar magnitude. [46,49] The natural logarithm of the average static polarizabilities of 1, 2, 3, and 4 predicted by the PBE0 using G09, Dujinen using the screening fac- Rearrangement each of these equations followed by inverting the natural logarithm to the exponential form gives: <α > = I s 1/m e −c/m , where m and c are the slope and the intercept, respectively; for instance, <α > = I s −0.61 e 7.38 from Equation 14.…”

Section: Optical Propertiesmentioning

confidence: 99%

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DFT and CIS(D) theoretical study on the ground and excited states of pentanitrogen cation

Mkadmh

2020

Int J of Quantum Chemistry

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Different isomers of N 5 + were modeled at DFT(PBE0)/aug-cc-pV(Q + d)Z, and their ground(transition) state characteristics were assessed through frequency calculations. Single-point energies were accomplished at PBE0/aug-cc-pV(5 + d)Z. Nonlinear optical susceptibilities (NLO) of isomers were accomplished using Firefly, while the linear optical invariant was examined using the finite-field method, Firefly, and modified dipole field tensor in the presence of two different screening factors. The excited states, singlets and triplets, of N 5 + 1 P + g were modeled at the CIS and CIS(D) and then their optical parameters were estimated at TDFT(PBE0)/aug-cc-pV(Q + d)Z using Firefly. The singlet N 5 + 1 P + g is found the most stable isomer, with the inversional rate constant larger than that of the Cs isomer and high energy barrier with the triplet counterpart. Isomers 2, 3, and 4 are found local minima, while 5 and 6 are saddle points: transition states between equivalent invertomers. Energy calculations of the singlet and triplet isomers were in excellent agreement with the literature. An excellent correlation is found between the average polarizability and the impulse factor. Substantial variations were found between the singlet and triplet excited states in terms of energy, geometry, and optical properties from one side and with N 5 + 1 P + g from the other side. Reactivity indices showed that N1 and N5 are the optimum nucleophilic and electrophilic reactivity sites.

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Section: Resultsmentioning

confidence: 99%

Section: Optical Propertiesmentioning

confidence: 99%

DFT and CIS(D) theoretical study on the ground and excited states of pentanitrogen cation

Mkadmh

2020

Int J of Quantum Chemistry

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“…N is calculated for a 9 Å radius sphere around each atom, where protein atoms are counted and excluded volume is populated by an appropriate number of waters. Assuming additivity of atom polarizabilities, α is then defined as the sum of individual polarizabilities for protein atoms and waters in the 9 Å radius sphere (see Methods, Table for atomic volumes and polarizabilities). Using these values, the calculated dielectric constant is 76 in a fully solvated sphere, consistent with the experimentally determined dielectric of bulk water .…”

Section: Resultsmentioning

confidence: 99%

“…We estimate the electrostatic free energy of peptides by solving for a local atomic dielectric environment using the dielectric constant form [see Eq. ], where N is a density in atoms per Å 3 and α is the additive isotropic atomic polarizability, for all atoms within 9 Å. Volumes for each atom were used to estimate how many water molecules can occupy the remaining volume.…”

Section: Methodsmentioning

confidence: 99%

Empirical estimation of local dielectric constants: Toward atomistic design of collagen mimetic peptides

Pike

Nanda

2015

Biopolymers

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One of the key challenges in modeling protein energetics is the treatment of solvent interactions. This is particularly important in the case of peptides, where much of the molecule is highly exposed to solvent due to its small size. In this study, we develop an empirical method for estimating the local dielectric constant based on an additive model of atomic polarizabilities. Calculated values match reported apparent dielectric constants for a series of Staphylococcus aureus nuclease mutants. Calculated constants are used to determine screening effects on Coulombic interactions and to determine solvation contributions based on a modified Generalized Born model. These terms are incorporated into the protein modeling platform protCAD, and benchmarked on a data set of collagen mimetic peptides for which experimentally determined stabilities are available. Computing local dielectric constants using atomistic protein models and the assumption of additive atomic polarizabilities is a rapid and potentially useful method for improving electrostatics and solvation calculations that can be applied in the computational design of peptides.

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“…So, it is not surprising to find theoretical data on systems studied in this work. 37 Nevertheless, pressure information is not available and models are generally not adapted to take into account this parameter. Automatic algorithms devoted to the calculation of local properties like individual polarizability under pressure must then be developed as detailed in the following.…”

Section: Appendix: Polarizability Quantum Calculationsmentioning

confidence: 99%

Concentration dependent refractive index of a binary mixture at high pressure

Croccolo

Arnaud

Bégué

et al. 2011

The Journal of Chemical Physics

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In the present work binary mixtures of varying concentrations of two miscible hydrocarbons, 1,2,3,4-tetrahydronaphtalene (THN) and n-dodecane (C12), are subjected to increasing pressure up to 50 MPa in order to investigate the dependence of the so-called concentration contrast factor (CF), i.e., (∂n/∂c) p,T , on pressure level. The refractive index is measured by means of a Mach-Zehnder interferometer. The setup and experimental procedure are validated with different pure fluids in the same pressure range. The refractive index of the THN-C12 mixture is found to vary both over pressure and concentration, and the concentration CF is found to exponentially decrease as the pressure is increased. The measured values of the refractive index and the concentration CFs are compared with values obtained by two different theoretical predictions, the well-known Lorentz-Lorenz formula and an alternative one proposed by Looyenga. While the measured refractive indices agree very well with predictions given by Looyenga, the measured concentration CFs show deviations from the latter of the order of 6% and more than the double from the Lorentz-Lorenz predictions.

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Atom additive model based on dipole field tensor to compute static average molecular dipole polarizabilities

Cited by 14 publications

References 32 publications

DFT and CIS(D) theoretical study on the ground and excited states of pentanitrogen cation

DFT and CIS(D) theoretical study on the ground and excited states of pentanitrogen cation

Empirical estimation of local dielectric constants: Toward atomistic design of collagen mimetic peptides

Concentration dependent refractive index of a binary mixture at high pressure

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