Intramolecular hydrogen bonding in ribonucleoside sugar hydroxyls. An abinitio study

1992 ◽  
Vol 70 (6) ◽  
pp. 1640-1644 ◽  
Author(s):  
Enric Bosch ◽  
Miquel Moreno ◽  
José M. Lluch
Keyword(s):  
Proton Transfer ◽  
Topological Analysis ◽  
Minimum Energy ◽  
Geometry Optimization ◽  
Intramolecular Hydrogen Bonding ◽  
Proton Transfer Reaction ◽  
Stationary Points ◽  
Energy Structure ◽  
Full Geometry Optimization ◽  
Intramolecular Hydrogen

Abinitio self-consistent field (SCF) calculations were done for a model of a ribonucleoside where only the ring part of the furanoside form of D-ribose is considered. Full geometry optimization and direct location of stationary points were used in order to characterize the geometry of the minimum energy structure and of the transition state for the proton transfer reaction in the anion. Topological analysis of the charge density and its Laplacian for the minimum energy structure allow us to find clear electronic and geometrical evidence of an intramolecular hydrogen bond. On the other hand, our results show a very low energy barrier for the proton transfer so that the proton jumps easily between the two oxygen atoms.

Conformation and electronic structure of Carbidopa. A QM/MD study

2016 ◽  
Vol 15 (01) ◽  
pp. 1650002
Author(s):  
Ghader M. Sukker ◽  
Nuha Wazzan ◽  
Ashour Ahmed ◽  
Rifaat Hilal
Keyword(s):  
Density Functional ◽  
Minimum Energy ◽  
Geometry Optimization ◽  
Md Simulations ◽  
Energy Structure ◽  
Functional Theory ◽  
Conformational Preferences ◽  
The Density Functional Theory ◽  
Quantum Chemical Topology ◽  
Bonding Characteristics

Carbidopa (CD) is a drug used in combination with L-dopa (LD) in treatment of Parkinson’s disease (PD). CD is an inhibitor for enzyme decarboxylase, yet its mode of action is not entirely known although it is believed to involve enzyme shape recognition. The present work attempts to investigate the conformational preferences of CD. Tight geometry optimization at the density functional theory (DFT)/B3LYP/6-311[Formula: see text]G** level of theory has been carried out. The shallow nature of the potential energy surface (PES) and the presence of several local minima within a small energy range necessitate the launching of DFT-based molecular dynamics (MD) simulations. Two MD experiments were submitted for 35,000 points each. The complete trajectory in time domain of 10.5 ps is analyzed and discussed. The global minimum energy structure of CD is localized and identified by subsequent frequency calculations. The quantum theory of atom in molecules (QTAIMs) is used to extract and compare the quantum chemical topology features of the electron density distribution in CD and LD. Bonding characteristics are analyzed and discussed within the natural bond orbital (NBO) framework.

First-Principles Geometry Optimization of Polysilane

1988 ◽  
Vol 141 ◽  
Author(s):  
John W. Mintmire
Keyword(s):  
Total Energy ◽  
First Principles ◽  
Density Functional ◽  
Local Density ◽  
Minimum Energy ◽  
Geometry Optimization ◽  
Functional Approach ◽  
Energy Structure ◽  
Atomic Orbitals ◽  
Local Density Functional

AbstractA first-principles approach is reviewed for calculating the total energy of chain polymers using a linear combination of atomic orbitals local-density functional approach. The geometry for the all-trans conformation of polysilane is optimized by finding the minimum energy structure using this method.

Experimental and theoretical charge density, intermolecular interactions and electrostatic properties of metronidazole

2019 ◽  
Vol 75 (6) ◽  
pp. 942-953 ◽  
Author(s):  
Chinnasamy Kalaiarasi ◽  
Christy George ◽  
Rajesh G. Gonnade ◽  
Venkatesha R. Hathwar ◽  
Kumaradhas Poomani
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Intermolecular Interactions ◽  
Topological Analysis ◽  
Intramolecular Hydrogen Bonding ◽  
Bond Critical Point ◽  
Monoclinic System ◽  
Electrostatic Properties ◽  
Negative Laplacian ◽  
Intramolecular Hydrogen

Metronidazole is a radiosensitizer; it crystallizes in the monoclinic system with space group P21/c. The crystal structure of metronidazole has been determined from high-resolution X-ray diffraction measurements at 90 K with a resolution of (sin θ/λ)max = 1.12 Å−1. To understand the charge-density distribution and the electrostatic properties of metronidazole, a multipole model refinement was carried out using the Hansen–Coppens multipole formalism. The topological analysis of the electron density of metronidazole was performed using Bader's quantum theory of atoms in molecules to determine the electron density and the Laplacian of the electron density at the bond critical point of the molecule. The experimental results have been compared with the corresponding periodic theoretical calculation performed at the B3LYP/6-31G** level using CRYSTAL09. The topological analysis reveals that the N—O and C—NO2 exhibit less electron density as well as negative Laplacian of electron density. The molecular packing of crystal is stabilized by weak and strong inter- and intramolecular hydrogen bonding and H...H interactions. The topological analysis of O—H...N, C—H...O and H...H intra- and intermolecular interactions was also carried out. The electrostatic potential of metronidazole, calculated from the experiment, predicts the possible electrophilic and nucleophilic sites of the molecule; notably, the hydroxyl and the nitro groups exhibit large electronegative regions. The results have been compared with the corresponding theoretical results.

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