From Democritus to Schrödinger: a reflection on quantum molecular modeling

Vasilescu, D.; Adrian-Scotto, Martine

doi:10.1007/s11224-010-9665-z

Cited by 12 publications

(3 citation statements)

References 111 publications

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“…Experimentally, it has been shown that gaseous HCN is partially polymerized at pressures beyond 1.3 GPa [24,25]. While there are many static calculations on the stability of HCN clusters [23,[26][27][28][29], only a few theoretical studies are available on the dynamic formation of HCN polymers [30,31].…”

Section: Introductionmentioning

confidence: 99%

High-pressure phases of hydrogen cyanide: formation of hydrogenated carbon nitride polymers and layers and their electronic properties

Khazaei

Liang

Bahramy

et al. 2011

J. Phys.: Condens. Matter

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We have performed a set of first-principles simulations to consider the possible phase transitions in molecular crystals of HCN under high pressure. Our calculations reveal several transition paths from the orthorhombic phase to tetragonal and then to triclinic phases. The transitions from the orthorhombic to the tetragonal phases are of the second order, whereas those from the tetragonal to the triclinic phases turn out to be of the first-order type and characterized by an abrupt decrease in volume. Our calculations show that, by adjustment of the temperature and pressure of the HCN molecular crystal, novel layered and polymeric crystals with insulating, semiconducting or metallic properties can be found. Based on our simulation results, two different crystal formation mechanisms are deduced. The stabilities of the predicted structures at ambient pressure are further assessed by performing phonon or MD simulations. In addition, the electron transport properties of the predicted polymers are obtained using the non-equilibrium Green's function technique combined with density functional theory. The results show that the polymers have metallic-like I-V characteristics.

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Section: Introductionmentioning

confidence: 99%

High-pressure phases of hydrogen cyanide: formation of hydrogenated carbon nitride polymers and layers and their electronic properties

Khazaei

Liang

Bahramy

et al. 2011

J. Phys.: Condens. Matter

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“…HOMO represents the ability to donate an electron, and LUMO acts as an electron acceptor. Therefore, the molecular properties describing the global reactivity and local selectivity of the molecule under study, such as electron affinity A = -E LUMO , ionization potential I = -E HOMO , electronegativity χ = (I + A)/2, and hardness η = (I -A)/2, may be assessed from the HOMO and LUMO energy values [27][28][29][30]. For thymogen, these calculated parameters are as follows: A = 1.710 eV, I = 6.278 eV, χ = 3.994 eV, η = 2.284 eV.…”

Section: Resultsmentioning

confidence: 99%

Structural Analysis and Molecular Docking Studies of Thymogen

2021

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Trp-OH), immunoactive dipeptide, was investigated by molecular modeling methods. The conformational profiles of this molecule were investigated by molecular mechanics method. Then obtained most stable conformations of this dipeptide were optimized using DFT/ B3LYP level of theory with 6-31+G(d,p) basis set. The structural characteristics, molecular electrostatic potential (MEP) map, highest occupied and lowest unoccupied molecular orbital energies, dipole moment (μ), polarizability (α) and other parameters characterized the molecular properties of thymogen were calculated. It was found that the conformation with extended form of backbone is optimal for this molecule. Moreover, thymogen was docking onto the specific T-cell receptor using AutoDock Vina software. It was shown that the optimized structure of thymogen calculated by DFT/B3LYP/6-31+G(d,p) gives a binding affinity value -7.9 kcal/mol, which points out that it complements well a cleft on the surface of the receptor shown to be the attachment site. On the basis of the received results the model of pharmacophore of thymogen for its interaction with T-cell receptor was proposed.

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“…Vasilescu and Adrian-Scotto [309] in their paper review the development of quantum molecular modeling from historical approach and atom concept to two essential ways used today, the ab initio and DFT methods with which, among others, conformational analysis, electrostatics, molecular spins and radicals, infrared and Raman spectra, thermochemistry, and electrophilicity properties can be derived.…”

Section: Issuementioning

confidence: 99%