An approach to estimate the energy and strength of the intramolecular hydrogen bond in different conformers of 4‐methylamino‐3‐penten‐2‐one

The molecular structure and intramolecular hydrogen bond energy of 32 conformers of 4‐methylamino‐3‐penten‐2‐one were investigated at MP2 and B3LYP levels of theory using the standard 6–31G** basis set and AIM analyses. Furthermore, calculations for all the possible conformations of 4‐methylamino‐3‐penten‐2‐one in water solution were also carried out at B3LYP/6–31G** level of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the ketoamine conformers of this compound are more stable than the other conformers (i.e., enolimine and ketoimine). This stability is mainly due to the formation of a strong N? H···O intramolecular hydrogen bond, which is assisted by π‐electrons resonance. Hydrogen bond energies for all conformers of 4‐methylamino‐3‐penten‐2‐one were obtained from the related rotamers method. The nature of intramolecular hydrogen bond existing within 4‐methylamino‐3‐penten‐2‐one has been investigated by means of the Bader theory of atoms in molecules, which is based on topological properties of the electron density. The results of these calculations support the results which obtained by related rotamers method. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Stabilization of an excess electron on molecular surfaces by a pair of HF molecules

This work presents the results of solvation of electrons on several hypothetical cyclooctane and cyclohexane molecular surfaces, using the hydrogen fluoride (HF) dimer. These complexes were constructed with extensive OH groups on one side of a hydrocarbon surface (i.e., cyclohexane sheets), which creates hydrogen‐bonded networks that can form, increasing the dipole moment of the system. Concurrently, the hydrogen atoms on the opposite side of the surface form a pocket of positive charge that can attract excess electrons. Two possible orientations for HF dimer solvation on eight molecular surfaces that have been demonstrated to be stable toward electron detachment are examined. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Formation of simple organic molecules in the interstellar medium

In this work we present a methodology for the synthesis of simple molecules from basic formaldehyde (H₂CO) precursors. We have approached this challenging problem by considering a basic dimerization scheme that eventually leads to diose and methyl formate, using an HCO⁺ proton source. This species was chosen due to its ample abundance in the atmosphere. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Construction of novel coordination polymers with simple ligands

Three different types of metal-organic polymers have been prepared by a solution diffusion process carried out at room temperature. Crystals of the copper coordination polymers [CuX(4,4′-bipy)] _n (X = Cl, Br, I) have been obtained by the reaction of 4,4′-bipyridine ligands with Cu₂X₂ fragments to yield a three-dimensional network consisting of four interlocking planar lattices. Single crystals of [Cu₂(1,2,4,5-BTC)(DMF)₂] _n (1,2,4,5-BTC = 1,2,4,5-benzene tetracarboxylate) have been grown by slow diffusion from solutions of a mixture of CuBr₂, 2,2′-dithiosalicylic acid, and sodium azide plus a mixture of 1,2,4,5-H₄BTC and 4-cyanopyridine. The complex [Co(1,3,5-BTC)(4,4′-bipy)] _n (1,3,5-BTC = 1,3,5-benzene tricarboxylate) has a 3D open framework structure involving terminal cobalt atoms plus bridging 1,3,5-BTC and 4,4′-bipyridine ligands.     

Localized electron traps on extended molecular surfaces

We have previously alluded to the fact that concentrated charge pockets can form on molecular surfaces that can act to stabilize excess electrons. These charge pockets are formed from systems, which posses a network of hydrogen bonded OH groups on one side of the surface and hydrogen atoms on the opposite side of the molecular surface. In this work, we have increased the size of our recently reported molecular surfaces (Jalbout and Adamowicz, Mol Phys, 2006, 19, 3101) while keeping the number of OH groups constant, to investigate localized charge concentration on extended frameworks. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

The effect of substitution on the intramolecular hydrogen bonding in 3‐hydroxy‐propenethial

The intramolecular hydrogen bond strength of 3‐hydroxy‐propenethial (HPT) as well as the fluoro, chloro, bromo, and methyl derivatives were investigated at the B3LYP/6‐311++G^** level of theory. Solvent‐based calculations (in water) for HPT and derivatives were also carried out. The nature of the intramolecular hydrogen bond existing within the molecular under investigation has been studied by means of the Bader theory of atoms in molecules (AIM) that is based upon the use topological properties in terms of the electron density. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Influences of Temperature and Solvent Ions in Solution on States and Properties of Deoxyribonucleic Acid (DNA)

We here study the influences of the temperature and solvent ions in solution on the states and properties of DNA by a new dynamical model. This model admits three degrees of freedom per base-pair: two displacement variables related to the vibrations of the hydrogen atom in the hydrogen bonds and base (nucleotide), respectively, and an angular variable related to the rotation of each base, which delineate different forms of motion of the hydrogen atom and bases and the relations among them. In this model we stress specially the important role of the hydrogen atom in the hydrogen bonds of the bases in the dynamics of DNA. According to their properties of motion we give the Hamiltonian of the system and the corresponding equations of motion, and find out their soliton solutions. The solitons formed by the displacements of the hydrogen atoms and bases and their rotations are the excitation states arising from the energy absorbed by the DNA working at the biological temperature. We give further the free energy of the thermal excitation state in DNA system by transfer integral way and find out the corresponding specific heat. The specific heat increases with the increasing of the temperature and concentration of the solvent ions in the solution, but is not linear changes in the region of high temperature. If compared with experimental data, they are approximately consistent. Meanwhile we find that the solvent ion concentration influences seriously on the stability, states, and configurations of DNA.     

The structures,thermochemistry, and electron affinities of hydrogenated silicon clusters Si6Hn/Si6H (n = 3–14)

The hydrogenated silicon clusters structures, electron affinities, and dissociation energies of the Si₆H_n/Si₆H (n = 3?14) species have been systematically investigated by means of three density functional theory (DFT) methods. The basis set used in this work is of double‐ζ plus polarization quality with additional diffuse s‐ and p‐type functions, denoted DZP++. The geometries are fully optimized with each DFT method independently. Three different types of energy separations presented in this work are the adiabatic electron affinity (EA_ad), the vertical electron affinity (EA_vert), and the vertical detachment energy (VDE). The first Si? H dissociation energies D_e (Si₆H_n→ Si₆H_n?1+H) for the neutral Si₆H_n and D_e (Si₆H→Si₆H+H) for the anionic Si₆H species have also been reported. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Intramolecular hydrogen bonding in 3‐imino‐propenylamine: Theoretical investigations

Intramolecular H‐bonds existing for derivatives of 3‐imino‐propenylamine have been studied using the B3LYP/6‐311++G** level of theory. The nature of these interactions, known as resonance‐assisted hydrogen bonds, has been discussed. Vibrational frequencies for α‐derivatives were calculated at the same level of theory. The topological properties of the electron density distributions for N? H···N intramolecular bridges have been analyzed in terms of the Bader theory of atoms in molecules (AIM). Calculation for 3‐imino‐propenylamine derivatives in water solution were also carried out at B3LYP/6‐311++G** level of theory. Finally, the analysis of hydrogen bond in this molecule and their derivatives by quantum theory of natural bond orbital methods fairly support the ab initio results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Theoretical study of molecular and electronic structure of 2‐Se‐(2‐methyl‐2‐propenyl)‐1‐benzoic acid

A theoretical study of 2‐Se‐(2‐methyl‐2‐propenyl)‐1‐benzoic acid was carried out to investigate the molecular and electronic structure of this molecule, using the B3LYP density functional theory (DFT) method with the 6‐311+G** basis set. The optimized geometry of the molecule was obtained for the ortho, meta, and para isomers of the complex. In addition, the theoretical vibrational spectrum is presented, and thermal corrections in the limit of 100–1,000 K are discussed using the Shomate thermodynamic equations. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007