Density functional theory study of conformational and opto-electronic properties of oligo-para-phenylenes (original) (raw)
Related papers
The Journal of Physical Chemistry B, 2009
The theoretical electronic spectrum of the tryptophan-phenylalanine bichromophoric dipeptide was obtained for one of the lowest-energy conformer by various high-level computational methods such as complete active space with second order perturbation theory, second-order approximate coupled-cluster theory, and timedependent density functional theory. The results show that the first excited state is located on the tryptophan residue and called L b state in the amino-acid. The second and third excited states correspond respectively to the L a state of Trp and the excited state in the Phe residue. Time-dependent density functional methods appeared to be not efficient to calculate the excited states of such a peptide (except the first one) due to the inclusion of charge transfer states.
Chemistry Proceedings
The goal of the present work was to evaluate the chemical reactivity of amino acids with polar uncharged side chains (serine, threonine, asparagine and glutamine) using density functional theory (DFT) and thermodynamics modeling by calculating a series of molecular descriptors and properties of their optimized geometries. The predictive calculations were achieved with Spartan software from Wavefunction, Inc. Irvine, CA, USA, hybrid algorithm B3LYP (Becke’s three-term functional; Lee, Yang, Parr exchange hybrid) and polarization basis set 6-31G(d,p) for equilibrium geometry at ground state in vacuum and in water, after energy minimization and geometry optimization. Thermodynamic properties (zero-point energy, enthalpy, constant volume heat capacity, entropy and Gibbs energy) for these derivatives were calculated and related to electrochemical ligand behavior. Reduction and oxidation potentials were correlated to their calculated energy levels for molecular orbitals.
A Theoretical Study of <i>β</i>-Amino Acid Conformational Energies and Solvent Effect
Open Journal of Physical Chemistry, 2015
The conformations of four β-amino acids in a model peptide environment were investigated using Hartree-Fock (HF) and density functional theory (DFT) methods in gas phase and with solvation. Initial structures were obtained by varying dihedral angles in increments of 45˚ in the range 0˚-360˚. Stable geometries were optimized at both levels of theory with the correlation consistent double-zeta basis set with polarization functions (cc-pVDZ). The results suggest that solvation generally stabilizes the conformations relative to the gas phase and that intramolecular hydrogen bonding may play an important role in the stability of the conformations. The β 3 structures, in which the R-group of the amino acid is located on the carbon atom next to the N-terminus, are somewhat more stable relative to each other than the β 2 structures which have the R-group on the carbon next to the carbonyl.
Density Functional Study of 2-[(R-Phenyl)amine]-1,4-naphthalenediones
Journal of Chemical Theory and Computation, 2007
The molecular and electronic structures of a series of 2-[(R-phenyl)amine]-1,4naphthalenediones (R) m-Me, p-Me, mEt , p-CF 3 , p-Hex, pEt , m-F, m-Cl, p-OMe, p-COMe, p-Bu, m-COOH, p-Cl, p-COOH, p-Br, m-NO 2 , m-CN, and p-NO 2) and their anions are investigated in the framework of density functional theory. The calculations are of all-electron type using a double zeta valence polarization basis set optimized for density functional theory methods. The theoretical study shows that all compounds are nonplanar. The nonplanarity can be rationalized in terms of occupied π orbitals. A linear correlation between the measured half-wave potentials and the calculated gas-phase electron affinities is found. It holds for local as well as generalized gradient corrected functionals. Structural parameters, harmonic vibrational frequencies, and adiabatic and vertical electron affinities as well as orbital and spin density plots of the studied compounds are presented.
International Journal of Molecular Sciences, 2004
Vertical ionization energies (IE) as a function of the conformation are determined at the quantum chemistry level for eighteen α-L-amino acids. Geometry optimization of the neutrals are performed within the Density Functional Theory (DFT) framework using the hybrid method B3LYP and the 6-31G**(5d) basis set. Few comparisons are made with wave-function-based ab initio correlated methods like MP2, QCISD or CCSD. For each amino acid, several conformations are considered that lie in the range 10-15 kJ/mol by reference to the more stable one. Their IE are calculated using the Outer-Valence-Green's-Functions (OVGF) method at the neutrals' geometry. Few comparisons are made with MP2 and QCISD IE. It turns out that the OVGF results are satisfactory but an uncertainty relative to the most stable conformer at the B3LYP level persists. Moreover, the value of the IE can largely depend on the conformation due to the fact that the ionized molecular orbitals (MO) can change a lot as a function of the nuclear structure.
Quantum-Chemical Description of Some Physical-Chemical Properties of Proteinogenic Amino Acids
Journal of Proteomics & Bioinformatics, 2018
We describe an impact of the inductive and steric effects of R-groups of amino acids on the reaction center (carboxy and amine groups) to estimate the propensity of amino acids for the peptide bond formation. These effects were quantitatively evaluated using the orders of the C-O and N-H bonds (PCO and PNH), the charges on the carbon, nitrogen and oxygen atoms of the carboxy, amine and hydroxy groups (q(C3), q(N6), q(O2)) and the dipole moments of all amino acids (μ). The calculations were carried out by means of modern quantum-chemical method Density Functional Theory (DFT). many-electron system can be determined by using functionals, which in this case is the spatially dependent electron density. Hence the name of density functional theory comes from the use of functionals of electron density. DFT is among the most popular and versatile methods available in computational biology. Unlike the wavefunction, which is not a physical reality, electron density is a physical characteristi...
Journal of Chemical Sciences, 2012
The characteristics of the intramolecular hydrogen bonding for a series of 19 different derivatives of β-aminoacroleine have been systematically analysed at the B3LYP/6-31G** level of theory. The topological properties of the electron density distributions for N-H ... O intramolecular bridges have been analysed by the Bader theory of atoms in molecules. The electron density (ρ) and Laplacian (∇ 2 ρ) properties at critical points of the relevant bonds, estimated by AIM calculations, showed that N-H ... O have low and positive character (∇ 2 ρ >0), consistent with electrostatic character of the hydrogen bond. The vibrational study of the hydrogen bonded systems showed negative (red) shifts for the ν (N−H) stretching mode. The πelectron delocalization parameter (Q) as a geometrical indicator of a local aromaticity and the geometry-based HOMA have also been calculated. Furthermore, the analysis of hydrogen bond in this molecule and its derivatives by natural bond orbital (NBO) methods support the DFT results. The results of AIM and NBO analysis as well as ν (N−H) were further used for estimation of the hydrogen bonding interactions and the forces driving their formation. The various correlations were found between geometrical, energetic and topological parameters. The substituent effect was also analysed and it was found that the strongest hydrogen bonds exist for N + (CH 3) 3 and Cl substituents while the weakest ones for COOCH 3 .
Density functional theory study of the conformation and energetics of silanol and disiloxane
Conformation-dependent properties of L-tyrosine and L-tryptophan in neutral and radical cations were studied by using the density functional theory (DFT) with a new density functional M05-2X. The results are compared with those obtained by using the conventional DFT (B3LYP). Results obtained by both types of DFT were in qualitative accord, including the existence of two conformational subgroups and their subgroupdependent adiabatic ionization energy and hydrogen bonding. On the other hand, quantitative differences were found between the two DFT methods as well: the M05-2X method successfully reproduced experimental adiabatic ionization energy, whereas the B3LYP functional consistently yielded significantly lower values by 0.2À0.3 eV. More importantly, natural bond orbital (NBO) analysis for cationic conformers showed that all conformers of L-tyrosine and L-tryptophan undergo charge localization upon ionization regardless of the presence of intramolecular hydrogen bonding, unlike the case of L-phenylalanine that was treated earlier by other studies. Different degrees of charge localization among all three aromatic amino acids are explained by employing a simple model in which the aromatic amino acid is assumed to consist of two submoieties of distinct cationic core: the backbone and aromatic side chain. The difference in adiabatic ionization energy between these two submoieties is found to govern the degree of charge localization.
2002
Ab initio methods are used to analyze the structure, energetics and binding energy of the four possible dipeptides that can be formed from alanine and glycine in gas phase. The structures of the peptides are optimized using Hartree±Fock, second-order Mùller±Plesset perturbation theory and density functional methods (DFT). The effect of electron correlation is analyzed with special emphasis on the calculated binding energies. Single-point energy calculations are performed with CCSD(T) on MP2 geometries to get some additional information on the correlation effects. Electron correlation effects and zero-point vibrational energy corrections increase the binding energy. At the highest level, CCSD(T), we ®nd that the binding energies for alanylalanine, alanylglycine, glycylalanine and glycylglycine are 4.86, 5.09, 5.61 and 5.89 kcal/mol, respectively. These numerical results suggest that glycine donates the OH group easier than alanine. A comparison between the Mùller±Plesset and DFT in different basis sets is made and gives indication of the usefulness of these methods for bio-molecules and peptide formation. Two functionals, B3LYP and B3P86 with different basis sets differing by the systematic inclusion of diffuse and polarization functions, are used in the DFT method. The results obtained using both functionals with a basis that includes both diffuse and polarization functions are in reasonable agreement with the Mùller±Plesset results. However, without including zero-point corrections, some DFT results lead to non-bonding of the peptide molecule.