van der Waals corrections to density functional theory calculations: Methane,ethane, ethylene,benzene, formaldehyde,ammonia, water,PBE, and CPMD

Parameters are developed for a practical application of the empirical van der Waals (vdW) correction infrastructure available in the CPMD density functional theory (DFT) code. The binding energy, geometry, and potential energy surface (PES) are examined for methane, ethane, ethylene, formaldehyde, ammonia, three benzene dimer geometries, and three benzene–water geometries. The vdW corrected results compare favorably with MP2 and CCSD(T) calculations near the complete basis set limits, and with experimental results where they are available.     

Vibrational investigation of 1-cyclopentylpiperazine: A combined experimental and theoretical study

FT-IR and Raman spectra of 1-cyclopentylpiperazine(1cppp)have been experimentally examined in the region of 4000–200cm-1.The optimized geometric parameters,conformational equilibria,normal mode frequencies and corresponding vibrational assignments of 1cppp(C9H18N2)are theoretically examined by means of B3LYP hybrid density functional theory(DFT)method together with 6-31++G(d,p)basis set.On the basis of potential energy distribution(PED)reliable vibrational assignments have been made and the thermodynamics functions,highest occupied and lowest unoccupied molecular orbitals(HOMO and LUMO)of 1cppp have been predicted.Calculations are employed for four different conformations in C1 and Cs point groups of 1cppp in gas phase.Comparison between the experimental and theoretical results indicates that B3LYP method is able to provide satisfactory results for predicting vibrational frequencies and the structural parameters,vibrational frequencies and assignments.Furthermore,C1(equatorial-axial)point group has been found as the most stable conformer of 1cppp.     

Endo[metallo] SWNT‐amino acid interactions: A theoretical study

We propose that an atom of calcium (Ca) which is an alkaline earth metal on encapsulation inside of a metallic armchair (5,5) (SWNT) species can have stronger amino acid interactions. From our calculations of various physical parameters we depict several configurations in which such an endo[metallo] SWNT can be modified by an internally placed Ca atom. Density functional theory (DFT) calculations reveal that the most favorable interactions of the SWNT system is with tryptophan, tyrosine, and phenylalanine that can be directly correlated to the backbone geometry of the amino acid species. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Li@C60 complexes with amino acids: A theoretical analysis

In this work, we explore the ability of the Li@C₆₀ fullerene to interact with amino acids at the DFT-BLYP/DND level of theory. The calculations suggest that the most favorable interactions of the fullerene is with arginine, leucine, and tryptophan which is related to the backbone structure of the corresponding amino acids. We propose correlations of the dissociation energies, HOMO/LUMO band gaps in relation to the computed quantum chemical behavior.     

Comparison of HF,HF + MP2, LDA,BLYP, and B3LYP band structures of the homopolypeptides

Ab initio HF, HF + MP2, LDA DFT, BLYP DFT, and B3LYP DFT calculations are compared in the case of 19 homopolypeptides in their β pleated sheet conformation. The results show that the B3LYP method provides good results for the fundamental gaps, as compared with the values estimated on the basis of available UV spectra and intermediate exciton calculations for PolyGly and PolyAla. The HF method gives the best agreement, using Koopman's theorem for the ionization potential, taking the calculated VB_max values in the HF case if one compares them with the experimental ionization potentials of the 19 amino acids measured by mass spectroscopy. Finally, how these methods might be improved to determine the most stable conformations of the homopolypeptides is outlined. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Nature of the interaction between ammonia derivatives and carbon disulfide. A theoretical investigation

The interactions between NH₃, its methylated and chlorinated derivatives and CS₂ are investigated by ab initio CCSD(T) and density functional BLYP‐D3 methods. The CCSD(T)/aug‐cc‐pVTZ calculated interaction energies of complexes characterized by the S···N chalcogen bonds range between ?1.71 and ?2.78 kcal mol^?1. The S···N bonds are studied by atoms in molecules, natural bond orbital, and noncovalent interaction methods. The lack of correlation between the interaction energies of methylated amines complexes and the electrostatic potential results from the lone pair effect in aliphatic amines. Different structures of CS₂ complexed with ammonia derivatives, stabilized by other than the S···N chalcogen bonds, are also predicted. These structures are characterized by interaction energies ranging between 1.15 and 3.46 kcal mol^?1. The results show that the complexing ability of CS₂ is not very high but this molecule is able to attack the electrophilic or nucleophilic sites of a guest molecule.     

[80]Fullerene–amino acid interactions: Theoretical insights

This work reports the interactions of a C₈₀ fullerene species with the 20 naturally occurring amino acids. As a result of the analysis of multiple configurations, we have determined that the most stable C₈₀ complexes form with thiol containing amino acids. The stabilities of the resulting complexes have been classified according to biochemical classifications that are used to develop trends among the calculated data. The computed trends in the dissociation energies are related to the backbone structure of the corresponding amino acids. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

The substitution effect on heavy versions of cyclobutadiene

The structural and electronic characteristics of the M₄R₄ with M = C, Si, Ge and R = H, F, Cl, OH, MgH, BH₂, NH₂ Li are studied by ab initio calculations based on density functional theory using the hybrid B3LYP functional and 6‐311++G* basis set. The results of natural bond orbital analysis (NBO), the analysis of structural parameters (bond lengths and bond angle, dihedral angle), atoms in molecules based theory (AIM) topological parameters such as the characteristics of bond critical points (electron densities and their Laplacians) leads to the conclusion that interamolecular interaction due with OH, MgH₂, and NH₂ substitutions are different from other derivatives. The cyclobutadiene ring and its heavy versions display very different geometrical structures. The cations and anions of C₄R₄, Si₄R₄, and Ge₄R₄ were studied to determine the effect of substitution on structure and stability. It has been shown that substitutions with ability of forming hydrogen bonds, bound to the silicon and germanium atoms are able to change the properties of the four‐member rings more than the other substitutions. Comprehensive analyses of calculated NICS (nucleus‐independent chemical shifts), polarizability, electrophilicity, and electron density are done. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Assessment of the OLYP and O3LYP density functionals for first-row transition metals

We have investigated the performance of the OLYP and O3LYP density functionals for predicting atomic excitation energies and ionization potentials, and bond dissociation energies, geometries, and vibrational frequencies for selected first-row transition metal compounds, including hydrides (MH) and singly charged methylene and methyl cations. The OLYP and O3LYP functionals are similar to the well-known BLYP and B3LYP functionals, respectively, but use a new optimized exchange functional (OPTX) developed by Handy and Cohen (Mol Phys 2001, 99, 403) in place of the standard B88 exchange. A previous study by us on organic reactions (J Chem Phys 2002, 117, 1331) indicated that both OLYP and O3LYP gave results for heats of reaction and barrier heights that were overall superior to those using the popular B3LYP functional. For transition metals, however, although OLYP is overall superior to BLYP for molecular calculations, it is inferior to B3LYP. O3LYP provides results for molecules of about the same quality as B3LYP. For atomic excitation and 4s ionization energies, unless relativistic effects are included, OLYP and O3LYP are clearly worse than both BLYP and B3LYP. There is thus no real incentive to use either OLYP or O3LYP in place of B3LYP for calculations involving first-row transition metals.