DFT conformational studies of alpha-maltotriose

Recent DFT optimization studies on alpha-maltose improved our understanding of the preferred conformations of alpha-maltose. The present study extends these studies to alpha-maltotriose with three alpha-D-glucopyranose residues linked by two alpha-[1-->4] bridges, denoted herein as DP-3's. Combinations of gg, gt, and tg hydroxymethyl groups are included for both "c" and "r" hydroxyl rotamers. When the hydroxymethyl groups are for example, gg-gg-gg, and the hydroxyl groups are rotated from all clockwise, "c", to all counterclockwise, "r", the minimum energy positions of the bridging dihedral angles (phi(H) and psi(H)) move from the region of conformational space of (-, -), relative to (0 degrees , 0 degrees), to a new position defined by (+, +). Further, it was found previously that the relative energies of alpha-maltose gg-gg-c and "r" conformations were very close to one another; however, the DP-3's relative energies between hydroxyl "c" or "r" rotamers differ by more than one kcal/mol, in favor of the "c" form, even though the lowest energy DP-3 conformations have glycosidic dihedral angles similar to those found in the alpha-maltose study. Preliminary solvation studies using COSMO, a dielectric solvation method, point to important solvent contributions that reverse the energy profiles, showing an energy preference for the "r" forms. Only structures in which the rings are in the chair conformation are presented here.     

DFT studies and AIM analysis of AlN-polycycles

The structure and properties of AlN-polycycles were studied by DFT (density functional theory) method. The results of calculations were obtained at B3LYP/6-311G(d, p) level on model species. Topological parameters such as electron density, its Laplacian, kinetic electron energy density, potential electron energy density, and total electron energy density at the ring critical points (RCP) from Bader’s ‘Atoms in molecules’ (AIM) theory were analyzed in detail. These results indicate a good correlation between ρ(3, +1), G(r), H(r), and V(r) averaged values and hardness of AlN-polycycles. The aromaticity of all molecules has been studied by nucleus-independent chemical shift. There is a linear correlation between ΣNICS(0.0)_molecule values and polarizability.     

DFT and TD‐DFT investigation of IR and UV spectra of solvated molecules: Comparison of two SCRF continuum models

We report the calculation of liquid‐phase infrared (IR) and ultraviolet (UV) spectra in the framework of the solute's response to the reaction field of several solvents. In particular, we compare these two properties for the multipolar expansion model developed in the Nancy continuum model (NCM) and the polarized continuum model (PCM) scheme developed in Pise and Naples. All calculations are carried out at the (TD‐)DFT/6–311G(2d,2p) level of theory. The cavity size used for modeling the solute effects on the IR and UV spectra are examined. To calibrate the solute cavity size, we have investigated the IR spectra of coumarin and of a set of 14 additional solutes of different size and polarity in several dielectrical surroundings. It turns out that: (i) PCM and NCM present an identical behavior when a common cavity is used to calibrate the models; and (ii) for both NCM and PCM models, the IR spectra are highly sensitive to the solute and solvent polarity. The UV/VIS investigation of coumarin derivatives demonstrates that both models provide close estimates of λ_max independent of the solute cavity size. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Molecular orbital and DFT studies of the alimemazine radical cation

Semiempirical molecular orbital methods including CNDO, MNDO, AM1 and PM3, and density function theory method B3LYP/3-21G(d) were employed in the study of the alimemazine radical cation. It was found that PM3 was much better than CNDO, MNDO and AM1 in the structural optimization. The bond lengths and bond angles by PM3 were close to the experimental data, and comparable with the results by the density function theory method.     

FTIR spectroscopy and DFT studies of carbosilane dendrimers

The FTIR spectra of G(3), G(4), and G(9) generations of polybutylcarbosilane dendrimers have been recorded and analyzed. The structural optimization and normal mode analysis were performed for G(1) generation on the basis of density functional theory (DFT). This calculation gave vibrational frequencies and infrared intensities for the t,t- and g,-g-conformers of the butyl terminal groups, attached to the same silicon atom. The g,-g-conformer is 5.83 kcal/mol less stable compared to t,t-conformer. Relying on DFT calculations a complete vibrational assignment is proposed for different parts of the studied dendrimers. The dependence of band full width at half height in the IR spectra on generation number is established. The IR spectra of carbosilane dendrimers at higher temperatures at the ambient air and isolated from atmosphere air were studied. At temperature 180 degrees C all studied carbosilane dendrimers are stable when contact with atmosphere is absent, in the air they oxidize and thus CO and SiO groups appear.     

DFT and experimental studies of the structure and vibrational spectra of curcumin

The potential energy surface of curcumin [1,7‐bis(4‐hydroxy‐3‐methoxyphenyl)‐1,6‐heptadiene‐3,5‐dione] was explored with the DFT correlation functional B3LYP method using 6‐311G* basis. The single‐point calculations were performed at levels up to B3LYP/6‐311++G**//B3LYP/6‐311G*. All isomers were located and relative energies determined. According to the calculation the planar enol form is more stable than the nonplanar diketo form. The results of the optimized molecular structure are presented and compared with the experimental X‐ray diffraction. In addition, harmonic vibrational frequencies of the molecule were evaluated theoretically using B3LYP density functional methods. The computed vibrational frequencies were used to determine the types of molecular motions associated with each of the experimental bands observed. Our vibrational data show that in both the solid state and in all studied solutions curcumin exists in the enol form. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Geometry and tautomerism of sapphyrin—DFT studies

The structure and total energy have been investigated, applying the density functional theory (DFT), for idealized sapphyrin derivatives, created by replacements of meso-phenyl groups of 5,10,15,20-tetraphenylsapphyrin or β-alkyl groups of decaalkylsapphyrin with hydrogens or two methyl groups, respectively. The following species have been considered: the dication of plain sapphyrin (SapH₅²⁺) 12,13-dimethylsapphyrin (12,13-DMSapH₃), 12,13-dimethylsapphyrin dication (12,13-DMSapH₅²⁺), and the 10,15-dimethylsapphyrin dication (10,15-DMSapH₅²⁺). To address the issue of tautomerization the calculations have been carried out for the six feasible distribution patterns of NH protons among the five nitrogen centers of the planar sapphyrin P0_i (i=1–6). The B3LYP/6-31G optimized bond lengths and angles of sapphyrin or (dimethylated sapphyrin) skeletons are in satisfactory agreement with X-ray crystallographic values determined for decaalkylsapphyrin dications. The calculated total energies, using the B3LYP/6-31G**//3-21G approach demonstrate that the plain sapphyrin and 12,13-dimethylsapphyrin dications favor the planar geometry of the macrocycle. Localization of the methyl groups at the 10,15-meso positions of sapphyrin reversed the order of stability leading to the energy preference for the inverted structure. Thus, this steric factor related to the meso substitution seems to be instrumental in the C pyrrolic ring inversion. The DFT calculation also provided the relative stability frame for the complex tautomeric equilibria of SapH₃ which involve six different forms. Their relative stability decreases in the range: {25-NH, 26-N, 27-NH, 28-NH, 29-N} P0₃>({25-NH, 26-N, 27-NH, 28-N, 29-NH} P0₁>{25-NH, 26-NH, 27-N, 28-NH, 29-N} P0₅>{25-N, 26-NH, 27-NH, 28-NH, 29-N} P0₂>{25-NH, 26-N, 27-N, 28-NH, 29-NH} P0₆>{25-N, 26-N, 27-NH, 28-NH, 29-NH} P0₄. The stability order can be qualitatively related to the number and the nature of the cis NH interactions present in the sapphyrin core.     

EPR and DFT studies of the one-electron reduction product of phospholium cations

Cyclic voltammetry and EPR spectroscopy show that cationic phospholium groups are good electron acceptors whose reduction leads to a neutral radical where the unpaired electron is mainly delocalized on the carbon atoms of the five-membered ring. DFT calculations together with the crystal structure of phospholiums indicate that the electron addition causes a drastic diminution of the exocyclic CPC angle. The SOMO of reduced phospholium is compared to the SOMO of the phosphole radical anion.     

DFT conformational studies of the HI‐6 molecule

A systematic study of the oxime HI‐6 [1‐(2‐hydroxyiminomethyl‐1‐pyridinium)‐1‐(4‐carboxy‐aminopyridinium)dimethyl ether] hydrochloride, which is one of the most promising antidotes against soman intoxication, was carried out using density functional theory with the B3LYP (Becke, Lee, Yang, and Parr) method and the 6‐31+G*, 6‐31+G*, and 6‐31+G** basis sets. Rotational barriers, equilibrium geometries, and charge distributions were calculated in order to investigate the role of the side chain for the larger oximes used as antidotes in the treatment of neurotoxic organophosphate poisoning. Also reported is the comparison between HI‐6 and pralidoxime (2‐PAM), a smaller oxime previously studied in our research group. It is shown that conformation minima for the protonated E isomer do not depend on the size of the side chain; on the other hand, this effect has a pronounced influence on the protonated Z isomer. For the unprotonated isomers, other effects, such as electrostatic interactions and resonance, should be taken into account in their conformational analysis. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

DFT studies and vibrational spectra of isoquinoline and 8-hydroxyquinoline

The geometry, frequency and intensity of the vibrational bands of isoquinoline (IQ) and 8-hydroxyquinoline (8-HQ) were obtained by the density functional theory (DFT) calculations with the B3LYP functional and 6-31 G* basis set. The vibrational spectral data obtained from the solid phase mid and far FT-IR and FT-Raman spectra of IQ and 8-HQ are assigned based on the results of the normal coordinate calculations. The observed and the calculated spectra are found to be in good agreement.     

DFT studies on the magnetic exchange across the cyanide bridge

Exchange coupling across the cyanide bridge in a series of novel cyanometalate complexes with CuII-NC-MIII (M = Cr and low-spin Mn, Fe) fragments has been studied using the broken-symmetry DFT approach and an empirical model, which allows us to relate the exchange coupling constant with sigma-, pi-, and pi*-type spin densities of the CN- bridging ligand. Ferromagnetic exchange is found to be dominated by pi-delocalization via the CN- pi pathway, whereas spin polarization with participation of sigma orbitals (in examples, where the dz2 orbital of MIII is empty) and pi* orbitals of CN- yields negative spin occupations in these orbitals, and reduces the CuII-MIII exchange coupling constant. When the dz2 orbital of MIII is singly occupied, an additional positive spin density appears in the sigma(CN) orbital and leads to an increase of the ferromagnetic Cu-NC-M exchange constant. For low-spin [MIII(CN)6]3- complexes, the dz2 orbital occupancy results in high-spin metastable excited states, and this offers interesting aspects for applications in the area of molecular photomagnetism. The DFT values of the exchange coupling parameters resulting from different occupations of the t2g orbitals of low-spin (t2g5) FeIII are used to discuss the effect of spin-orbit coupling on the isotropic and anisotropic exchange coupling in linear Cu-NC-Fe pairs.     

DFT studies of the structure and vibrational spectra of 8-hydroxyquinoline N-oxide

The geometry, frequency and intensity of the vibrational bands of 8-hydroxyquinoline N-oxide (8-HQNO) and its deuterated derivative (8-DQNO) were obtained by the density functional theory (DFT) with the BLYP and B3LYP functionals and 6-31G(d,p) basis set. The optimized bond lengths and bond angles are in good agreement with the X-ray data. The IR and INS spectra of 8-HQNO and 8-DQNO computed at the DFT level reproduce the vibrational wavenumbers and intensities with an accuracy, which allows reliable vibrational assignments.     

Molecular dynamics and continuum electrostatics studies of inactivation in the HERG potassium channel

Fast inactivation of the HERG potassium channel plays a critical role in normal cardiac function. Malfunction of these channels due to either genetic mutations or blockade by drugs leads to cardiac arrhythmias. An unusually long S5-P linker in the outer mouth of HERG is implicated in the fast inactivation mechanism. To examine the role of the S5-P linker in this inactivation mechanism, we study the permeation properties of the open and inactive states of a recent homology model of HERG. This model was constructed using the KcsA potassium channel as a template and contains specific conformations of the S5-P linker in the open and inactive states. We perform molecular dynamics simulations on the HERG model, followed by free energy, structural, and continuum electrostatics calculations. Our free energy calculations lead to selectivity results of the model channel (K+ over Na+) that are different in some respects from those of other potassium channels but consistent with experimental observations. Our structural results show that, in the inactive state, the S5-P linkers move closer to the channel axis, possibly causing a steric hindrance to permeating K+ ions. Our electrostatics calculations reveal, in the inactive state, an electrostatic potential energy barrier of approximately 14 kT at the extracellular pore entrance, again sufficient to stop K+ ion permeation through the pore. These results suggest that a steric and/or electrostatic plug mechanism contributes to inactivation in the HERG homology model.     

Conformational studies of bipyrimidine-based mesogens by combination of DFT calculations and temperature-dependent infrared studies

Combination of DFT calculations and solid-state temperature-dependent infrared spectroscopy has confirmed that the central core of recently developed bipyrimidine-based mesogens is not flat, i.e. do not adopt a disc shape, inside the columnar liquid-crystalline phase. For this purpose, the intensities and the frequency shifts of the most sensitive C–N and C–C bands of the central bipyrimidine core have been studied as a function of the temperature and of the dihedral angle. The results support the reported packing model in which the molecules are interdigitated alternatively along their long axis and their short axis to form columns inside the mesophase.     

DFT studies on the favored and rare tautomers of neutral and redox cytosine

The complete tautomeric mixture consisting of nine prototropic tautomers has been studied in the gas phase at the DFT(B3LYP)/6-311+G(d,p) level for neutral, oxidized, and reduced cytosine. Rotational isomerism of the exo –OH group and geometrical isomerism of the exo =NH group have also been considered. Tautomeric conversions possible for cytosine have been compared with those for its structural models, 4-amino- and 2-hydroxypyrimidine. Effects of intramolecular interactions between neighboring groups for cytosine are analogous to those observed for model compounds. Although they are not very strong, they are sufficient to influence tautomeric equilibria and relative stabilities of individual tautomers. One-electron oxidation and one-electron reduction change tautomeric preferences. Tautomers that are rare forms for neutral cytosine become favored ones for oxidized and reduced cytosine. Aromaticity is not the main factor that dictates the tautomeric preferences. Stability of functional groups seems to be more important than full electron delocalization.     

DFT studies of cation binding by ��-cyclodextrin

Interactions of the ??-cyclodextrin (??-CD) ligand with Na⁺, Cu⁺, Mg²⁺, Zn²⁺, and Al³⁺ cations were investigated using density functional theory modeling. The objective of this study was to give insight into the mechanism of cation complexation. Two groups of conformers were found. The first group preserved the initial orientation of glucopyranose residues inside the ??-CD ligand. The mutual orientation of glucopyranose residues was strongly affected by the cation in the second group of conformers. The system interaction energy was decomposed into electrostatic (ES), Pauli and orbital contributions using the Ziegler?CRauk energy partitioning scheme. The total electrostatic energy, i.e., the sum of ES energy and polarization energy, is the dominating term in the interaction energy. In vacuum, the complexes formed with Al³⁺ were found to be more stable than with di- and monocations. The vacuum stability sequence was changed in aqueous solution.     

DFT theoretical studies of alkali metal acetylenic thiolates

It follows from DFT calculations of acetylenic thiolates and their structural isomers—thioketenes and thiirenes that only the acetylenic type is stable. Most of the negative charge is concentrated on the sulfur atom. The influence of the cation (Li, Na, K) and the acetylenic substituent on the electronic structure and geometry of the thiolates is investigated. DFT calculations of IR and ¹³C NMR spectra of phenylethynethiolate potassium are in agreement with experimental data.     

Ab initio and DFT studies on hydrolyses of phosphorus halides

Hydrolyses of phosphorus halides, (RO)(2)POX where R = H or Me and X = F or Cl, in the gas phase and in the reaction field have been investigated theoretically with ab initio and the density functional theory (DFT). The free energy of activation in the reaction field was also estimated using the Onsager method with a correction of entropy change and basis set superposition error (BSSE). The reaction of (MeO)(2)POF proceeds through a path with bifunctional catalysis regardless of the medium, but the reaction of (MeO)(2)POCl proceeds through bifunctional and general base catalysis in the gas phase and in water, respectively. The estimated free energy barrier of 23 kcal/mol for the hydrolysis of (MeO)(2)POF is in good agreement with the experimental values of 24 kcal/mol, and relative barrier of 3 kcal/mol to the (MeO)(2)POCl is also in good agreement with the experimental values of 5 kcal/mol of diisopropyl phosphorus halides ((Pr(i)O)(2)POX, X = F and Cl).     

DFT calculation and Raman excitation profile studies of benzophenone molecule

Excitation profiles of different Raman bands of benzophenone molecule have been critically analysed. Structural and symmetry properties of the molecule in different electronic states have been investigated. The possibility of existence of an excited electronic state in the region bellow 200 nm has been explored. Calculations on isolated molecule in gas phase have been performed with the use of density functional theory to correlate the observed vibrational spectra. The time dependent density functional theory has used to determine the singlet excitation energies. The optimized structural parameters have also been computed.