Methylation of zebularine investigated using density functional theory calculations

Deoxyribonucleic acid (DNA) methylation is an epigenetic phenomenon, which adds methyl groups into DNA. This study reveals methylation of a nucleoside antibiotic drug 1‐(β‐D ‐ribofuranosyl)‐2‐pyrimidinone (zebularine or zeb) with respect to its methylated analog, 1‐(β‐D ‐ribofuranosyl)‐5‐methyl‐2‐pyrimidinone (d5) using density functional theory calculations in valence electronic space. Very similar infrared spectra suggest that zeb and d5 do not differ by types of the chemical bonds, but distinctly different Raman spectra of the nucleoside pair reveal that the impact caused by methylation of zeb can be significant. Further valence orbital‐based information details on valence electronic structural changes caused by methylation of zebularine. Frontier orbitals in momentum space and position space of the molecules respond differently to methylation. Based on the additional methyl electron density concentration in d5, orbitals affected by the methyl moiety are classified into primary and secondary contributors. Primary methyl contributions include MO8 (57a), MO18 (47a), and MO37 (28a) of d5, which concentrates on methyl and the base moieties, suggest certain connection to their Frontier orbitals. The primary and secondary methyl affected orbitals provide useful information on chemical bonding mechanism of the methylation in zebularine. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Benchmark density functional theory calculations for nanoscale conductance

We present a set of benchmark calculations for the Kohn-Sham elastic transmission function of five representative single-molecule junctions. The transmission functions are calculated using two different density functional theory methods, namely an ultrasoft pseudopotential plane-wave code in combination with maximally localized Wannier functions and the norm-conserving pseudopotential code SIESTA which applies an atomic orbital basis set. All calculations have been converged with respect to the supercell size and the number of k|| points in the surface plane. For all systems we find that the SIESTA transmission functions converge toward the plane-wave result as the SIESTA basis is enlarged. Overall, we find that an atomic basis with double zeta and polarization is sufficient (and in some cases, even necessary) to ensure quantitative agreement with the plane-wave calculation. We observe a systematic downshift of the SIESTA transmission functions relative to the plane-wave results. The effect diminishes as the atomic orbital basis is enlarged; however, the convergence can be rather slow.     

Recent applications of density functional theory calculations to biomolecules

The purpose of this overview is to highlight the broad scope and utility of current applications of density functional theory (DFT) methods for the study of the properties and reactions of biomolecules. This is illustrated using examples selected from research carried out within our research group and in collaboration with others. The examples include the hyperfine coupling constants of amino acid radicals, the use of an amino acid as a chiral catalyst for the formation of carbon–carbon bonds in the aldol reaction, hydrogen-bond mediated catalysis of an aminolysis reaction, radiation-induced protein–DNA cross-links, and the mechanism by which an antitumor drug cleaves DNA. We demonstrate that DFT-based methods can be applied successfully to a broad range of problems that remain beyond the scope of conventional electron-correlation methods. Furthermore, we show that contemporary computational quantum chemistry complements experiment in the study of biological systems. Received: 19 December 2001 / Accepted: 8 April 2002 / Published online: 4 July 2002     

Lithium adsorption on graphite from density functional theory calculations

The structural, energetic, and electronic properties of the Li/graphite system are studied through density functional theory (DFT) calculations using both the local spin density approximation (LSDA), and the gradient-corrected Perdew-Burke-Ernzerhof (PBE) approximation to the exchange-correlation energy. The calculations were performed using plane waves basis, and the electron-core interactions are described using pseudopotentials. We consider a disperse phase of the adsorbate comprising one Li atom for each 16 graphite surface cells, in a slab geometry. The close contact between the Li nucleus and the graphene plane results in a relatively large binding energy (larger than 1.1 eV). A detailed analysis of the electronic charge distribution, density difference distribution, and band structures indicates that one valence electron is entirely transferred from the atom to the surface, which gives rise to a strong interaction between the resulting lithium ion and the cloud of pi electrons in the substrate. We show that it is possible to explain the differences in the binding of Li, Na, and K adatoms on graphite considering the properties of the corresponding cation/aromatic complexes.     

Conformational studies of Zn-Ligand-Hexose diastereomers using ion mobility measurements and density functional theory calculations

Ion mobility studies and density functional theory calculations were used to study the structures of [Zn/diethylenetriamine/Hexose/Cl]+ complexes in an effort to probe differences in the three-dimensional conformations. This information allows us to gain insight into the structure of these complexes before collisional activation, which is the first step in understanding the stereoselective dissociations observed under collisionally activated conditions. The collision cross sections obtained from the ion mobility measurements showed that the mannose structure is more compact than the galactose and glucose complexes, respectively. Using density functional theory, candidate structures for each of the experimentally observed complexes were generated. Two criteria were used to determine the most likely structures of these complexes before activation: (1) The allowed relative energies of the molecules (between 0-90 kJ/mol) and (2) collision cross section agreement (within 2%) between the theoretically determined structures and the experimentally determined cross section. It was found that the identity of the monosaccharide made a difference in the overall conformation of the metal-ligand-monosaccharide complex. For glucose and galactose, metal coordination to O(6) was found to be favorable, with the monosaccharide occupying the 4C1 chair conformation, while for mannose, O(2) metal coordination was found with the monosaccharide in a B3,0 conformation. Coordination numbers varied between four and six for the Zn(II) metal centers. Given these results, it appears that the stereochemistry of the monosaccharide influences the conformation and metal coordination sites of the Zn(II)/monosaccharide/dien complex. These differences may influence the dissociation products observed under collisionally activated conditions.     

Theoretical Auger electron spectra of polymers by density functional theory calculations using model dimers

We propose a new approach for analysis of Auger electron spectra (AES) of polymers by density functional theory (DFT) calculations with the Slater's transition-state concept. Simulated AES and X-ray photoelectron spectra (XPS) of four polymers [(CH2CH2)n (PE), (CH2CH(CH3))n (PP), (CH2CH(OCH3))n (PVME), and (CH2CH(COCH3))n (PVMK)] by DFT calculations using model dimers are in a good accordance with the experimental ones. The experimental AES of the polymers can be classified in each range of 1s-2p2p, 1s-2s2p, and 1s-2s2s transitions for C KVV and O KVV spectra, and in individual contributions of the functional groups from the theoretical analysis.     

Studies on the encapsulation of various anions in different fullerenes using density functional theory calculations and Born-Oppenheimer molecular dynamics simulation

The density functional theory (DFT)-based Becke's three parameter hybrid exchange functional and Lee-Yang-Parr correlation functional (B3LYP) calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations have been performed to understand the stability of different anions inside fullerenes of various sizes. As expected, the stability of anion inside the fullerene depends on its size as well as on the size of the fullerene. Results show that the encapsulation of anions in larger fullerenes (smaller fullerene) is energetically favorable (not favorable). The minimum size of the fullerene required to encapsulate F(-) is equal to C(32). It is found from the results that C(60) can accommodate F(-), Cl(-), Br(-), OH(-), and CN(-). The electron density topology analysis using atoms in molecule (AIM) approach vividly delineates the interaction between fullerene and anion. Although F(-)@C(30) is energetically not favorable, the BOMD results reveal that the anion fluctuates around the center of the cage. The anion does not exhibit any tendency to escape from the cage.     

Spectral analysis of acetylcholine halides by density functional theory calculations

The optimized molecular structures, vibrational frequencies and ¹H and ¹³C NMR chemical shifts of acetylcholine halides (F, Cl, and Br) have been investigated using density functional theory (B3LYP) method with 6-311G(d) basis set. The comparison of their experimental and calculated IR, R and NMR spectra of the compounds has indicated that the spectra of three optimized minimum energy conformers can simultaneously exist in one experimental spectrum. Thus, it was concluded that the compounds simultaneously exist in three conformations in the ground state. The calculated optimized geometric parameters (bond lengths and bond angles), vibrational frequencies and NMR chemical shifts for the minimum energy conformers were seen to be in a good agreement with the corresponding experimental data. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program.     

Prediction of cellulose nanotube models through density functional theory calculations

We report the generation of a nano-scale tubular structure of cellulose molecules (CelNT), through density functional theory (DFT) calculations. When a cellulose III_I (1 0 0) chain sheet model is optimized by DFT calculations, the sheet models spontaneously roll into tubes. The oligomers arrange in a right-handed, four-fold helix with one-quarter chain staggering, oriented with parallel polarity similar to the original crystal structure. Based on a one-quarter chain staggering relationship, six large CelNT models, consisting of 16 cellulose chains with DP = 80, are constructed by combinations of two types of chain polarities and three types of symmetry operations to generate a circular arrangement of molecular chains. All six CelNT models are examined by molecular dynamics (MD) calculations in chloroform. While four CelNT models retain a tubular form throughout MD calculations, the remaining two deform. 3D-RISM theory model is used to estimate the solvation free energies of the four CelNT models. The results suggest that the CelNT model with a chain arrangement of parallel polarity and right-handed helical symmetry forms the most stable tube structure.     

Prediction of formation constants of metal-ammonia complexes in aqueous solution using density functional theory calculations

Density functional theory calculation of gas-phase Delta G of replacement of a water molecule by NH(3) on [M(H(2)O)(6)](n+)(g) for 19 different metal ions correlates well with Delta G of formation of mono NH(3) complexes of these ions in water, suggesting this approach will permit prediction of formation constants in aqueous solution, and produce insights into theories of metal complex formation reactions.     

Revealing the way of self-complementary dimerization for a shape-persistent macrocycle using density functional theory calculations

A preferred geometry of a planar shape-persistent dimeric macrocycle with diacetylene-linked alternating hexylbenzene and perfluorobenzene rings is revealed by resolving its three-dimensional spatial energy profile using density functional theory calculations. The resulting dimer exhibits a face-to-face geometry with about 51.5 degrees rotational off-set around the principal axis and an intermolecular distance of about 3.91 A. The calculated intermolecular interaction energy and the 1H NMR chemical shifts of the exo- and endo-annular protons of the predicted dimer agree very well with the recent experimental data. More importantly, the current study resolves the ambiguity observed in the experiment pertaining to how the dimer would form, and provides insight for predicting the geometry of similar dimeric macrocycles or other pi-pi interacting systems.     

Time-dependent density functional theory calculations of the photoabsorption of fluorinated alkanes

Time-dependent density functional theory (TD-DFT) calculations of the transition energies and oscillator strengths of fluorinated alkanes have been performed. The TD-DFT method with the non-local B3LYP potential yields transition energies for the methanes, which are smaller by about 10% as compared to the experimental values. An empirical linear correlation was found between the calculated and experimental transition energies both at the B3LYP/DZ+Ryd(C, F) and B3LYP/cc-pVTZ+Ryd(C, F, H) levels for a total of 19 transitions of the fluorinated methanes with linear correlation coefficients of 0.987 for the former and 0.988 for the latter. This empirical correlation for fluorinated methane molecules is found to agree well with the previously obtained empirical correlations between calculated and experimental values for non-fluorinated molecules. The results show that a single empirical-correlation relationship can be used for both non-fluorinated and fluorinated molecules to predict transition energies. This linear relationship is then used to predict the photoabsorption spectra of ethane, propane, butane, and partially and fully fluorinated derivatives. A key result of these calculations is the dominance of Rydberg transitions in the spectral region of interest.     

Robust acceleration of self consistent field calculations for density functional theory

We show that the type 2 Broyden secant method is a robust general purpose mixer for self consistent field problems in density functional theory. The Broyden method gives reliable convergence for a large class of problems and parameter choices. We directly mix the approximation of the electronic density to provide a basis independent mixing scheme. In particular, we show that a single set of parameters can be chosen that give good results for a large range of problems. We also introduce a spin transformation to simplify treatment of spin polarized problems. The spin transformation allows us to treat these systems with the same formalism as regular fixed point iterations.     

Matrix infrared spectra and density functional theory calculations of molybdenum hydrides

Laser-ablated Mo atoms react with H2 upon condensation in excess argon, neon, and hydrogen. The molybdenum hydrides MoH, MoH2, MoH4, and MoH6 are identified by isotopic substitution (H2, D2, HD, H2 + D2) and by comparison with vibrational frequencies calculated by density functional theory. The MoH2 molecule is bent, MoH4 is tetrahedral, and MoH6 appears to have the distorted trigonal prism structure.     

Basis set dependence of phosphate frequencies in density functional theory calculations

The addition of extravalence, polarization and diffuse functions, were studied in order to conclude how they affect the P? O stretching frequencies of several biological relevant phosphate molecules. The results show that the polarization and the diffuse functions have opposite effects on the frequencies: the polarization functions downshift while the diffuse functions upshift the frequencies. The effect of the valence functions was more difficult to interpret. The effect of the conductor‐like screening model (CPCM)‐continuum model was also studied. The results show that the CPCM‐continuum model has a substantial effect on the frequencies for these small molecules. The continuum model's efficiency is mainly due to its effect on the geometries and not on the frequencies. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Basis set convergence of explicitly correlated double-hybrid density functional theory calculations

The basis set convergence of explicitly correlated double-hybrid density functional theory (DFT) is investigated using the B2GP-PLYP functional. As reference values, we use basis set limit B2GP-PLYP-F12 reaction energies extrapolated from the aug(')-cc-pV(Q+d)Z and aug(')-cc-pV(5+d)Z basis sets. Explicitly correlated double-hybrid DFT calculations converge significantly faster to the basis set limit than conventional calculations done with basis sets saturated up to the same angular momentum (typically, one "gains" one angular momentum in the explicitly correlated calculations). In explicitly correlated F12 calculations the VnZ-F12 basis sets converge faster than the orbital A(')VnZ basis sets. Furthermore, basis set convergence of the MP2-F12 component is apparently faster than that of the underlying Kohn-Sham calculation. Therefore, the most cost-effective approach consists of combining the MP2-F12 correlation energy from a comparatively small basis set such as VDZ-F12 with a DFT energy from a larger basis set such as aug(')-cc-pV(T+d)Z.     

Electron-structure calculations and bond order analysis using density functional theory of cationic dinuclear arene ruthenium complexes

The structure and nature of the metal-metal bonding interaction in the cationic complexes [(eta6-C6Me6)2Ru2(mu2-H)3]+ (1), [(eta6-C6Me6)2Ru2(mu2-H)2(mu2-1,4-SC6H4Br)]+ (2), [(eta6-C6Me6)2Ru2(mu2-H)(mu2-1,4-SC6H4Br)2]+ (3), and [(eta6-C6Me6)2Ru2(mu2-1,4-SC6H4Br)3]+ (4) have been studied at the density functional theory (DFT) level using molecular orbital (MO) theory, bond order (BO) analysis, bond decomposition energy (BDE), electron localization function (ELF), and Laplacian of the density methods. The results show that there is no direct bond between the two ruthenium atoms in 1-4, the MO interaction within the diruthenium backbone being stabilized by the bridging ligands. For complex 1, the ELF clearly shows that the bond within the diruthenium backbone is through the three bridging hydride ligands, which act as a sort of glue by forming three-center two-electron bonds characterized by (Ru, H, Ru) basins with 1.8 e mostly located in the H atomic basin.     

Projected gradient algorithms for Hartree-Fock and density matrix functional theory calculations

We present projected gradient algorithms designed for optimizing various functionals defined on the set of N-representable one-electron reduced density matrices. We show that projected gradient algorithms are efficient in minimizing the Hartree-Fock or the Muller-Buijse-Baerends functional. On the other hand, they converge very slowly when applied to the recently proposed BBk (k=1,2,3) functionals [O. Gritsenko et al., J. Chem. Phys. 122, 204102 (2005)]. This is due to the fact that the BBk functionals are not proper functionals of the density matrix.     

Periodic Hartree-Fock and density functional theory calculations for Li-doped polyacetylene chains

We have performed periodic restricted Hartree-Fock/6-31G** and B3LYP6-31G** density functional theory calculations on Li-doped trans-polyacetylene at various dopant concentrations, using C(2m)H(2m)Li2 unit cells (m = 7-14). Except for maintaining P1 rod symmetry the geometry was completely optimized for both uniform and nonuniform doping structures. In addition to geometry we obtain atomic charges, along with soliton formation and dopant binding energies, as well as band structures and densities of states. A thorough analysis of the band structure and density of states, as a function of dopant concentration, is presented. We also characterize the complex nature of the binding interaction between Li and the polyacetylene chain.