Conformational study of erythritol and threitol in the gas state by density functional theory calculations

Density functional theory calculations using the B3LYP functional and the 6-311++G(d,p) basis set were carried out on the isolated molecules of erythritol and L-threitol. For the meso isomer, a relatively large number of conformers have to be considered to describe the gas state structure. The lowest energy conformer is characterized by the establishment of a strong intramolecular H-bond between the two terminal hydroxyl groups, giving rise to a seven-membered ring and two additional weaker H-bonds between vicinal OH groups. In the case of L-threitol, two conformers are predominant in the gas state, and both are stabilized by the formation of a cyclic system of four intramolecular hydrogen bonds involving all OH groups. The conformational stability in both diastereomers is discussed in terms of the electronic energy and of the Gibbs energy. The weighted mean enthalpy of both diastereomers in the gas state at 298.15 K was obtained from the thermodynamic data and Boltzmann populations of the low-energy conformers.     

Conformational preferences of 1,4,7-trithiacyclononane: a molecular mechanics and density functional theory study

Conformational preferences of 1,4,7-trithiacyclononane were studied using a highly efficient sampling technique based on local nonstochastic deformations and the MM2(91) force field. The results show that conformers that the molecule adopts in the crystal state were found to be low-energy conformers (LECs) within 5 kcal mol(-1) of the global minimum. A conformation with C1 symmetry was the global minimum and the C3 and C2 conformations were calculated to be 0.03 and 1.78 kcal mol(-1) higher in energy, respectively. The structures were further minimized using Density Functional Theory (DFT) calculations with two different functionals. The C2 and the C1 conformations were found to be LECs with the C3 conformation more than 4.0 kcal mol(-1) above the global minimum. The relative energies and structural ordering obtained using the BP86 functional are in agreement with the previously reported relative energies calculated using second-order Moller-Plesset (MP2) ab initio calculations. With the energy ordering being dependent on the molecular mechanics force field used, the approach of MM-->DFT (searching exhaustively the available conformational space at the MM level followed by generating the energy ordering through DFT calculations) appears to be appropriate for thiacrown ethers.     

Inter- versus intra-molecular cyclization of tripeptides containing tetrahydrofuran amino acids: a density functional theory study on kinetic control

Density functional B3LYP method was used to investigate the preference of intra- and inter-molecular cyclizations of linear tripeptides containing tetrahydrofuran amino acids. Two distinct model pathways were conceived for the cyclization reaction, and all possible transition states and intermediates were located. Analysis of the energetics indicate intermolecular cyclization being favored by both thermodynamic and kinetic control. Geometric and NBO analyses were performed to explain the trends obtained along both the reaction pathways. Conceptual density functional theory-based reactive indices also show that reaction pathways leading to intermolecular cyclization of the tripeptides are relatively more facile compared to intramolecular cyclization.     

基于密度泛函理论研究Watson–Crick碱基对中的氢键特征(英文)

基于密度泛函理论(DFT)研究腺嘌呤、胸腺嘧啶、鸟嘌呤、胞嘧啶以及腺嘌呤胸腺嘧啶碱基对、鸟嘌呤胞嘧啶碱基对。在DFT-B3LYP/6-31G**水平上利用自然键轨道理论分析研究结果显示,互补碱基对的结构和电子特征有利于氢键的形成。本文中讨论几何结构、电子结构、分子轨道和能量对于氢键形成的影响。此研究结果将有助于更好的理解AT和GC碱基对中氢键与它们的结构特性之间的关系。     

Studying the chemical reactivity properties of the target tumor-environment tripeptides NGR (asparagine-glycine-arginine) and RGD (arginine-glycine-aspartic acid) in their interactions with tamoxifen through conceptual density functional theory

Here, we report theoretical research into the interaction of the drug tamoxifen drug with tripeptides found in the tumor environment—specifically, asparagine-glycine-arginine (NGR) and arginine-glycine-aspartic acid (RGD). Reactivity parameters of these tripeptides were calculated and their intrinsic reactivities and cross-reactivities were analyzed. The interactions of the tripeptides with the nanodiamond–tamoxifen (ND-TAM) complex where the nanodiamond acts as a nanocarrier were also examined theoretically. In addition, their intestinal absorption was predicted based on the polar surface area. The results showed that tamoxifen interacts with RGD, and this interaction remained after the addition of the nanodiamond. An analysis of the chemical hardnesses of the tripeptides was carried out to explore their possible use as synthetic vectors when joined to the nanodiamond. Results indicated that NGR is the most stable of the tripeptides and could be used for active targeting. All calculations were implemented using the conceptual framework of density functional theory.     

Conformational study of asialo-GM1 (GA1) ganglioside

In order to investigate the significance of preferred conformations of the saccharide for the steric orientation and recognition of glycosphingolipids at the membrane surface, the conformational free energy calculations were carried out on the asialo-GM1 [GA1; β-D -Gal(1 → 3) β-D -GalNAc(1 → 4) β-D -Gal(1 → 4) β-D -Glc-O-ceramide] using a new program CONCARB (CONformational study program for CARBohydrate) in the unhydrated and hydrated states. The overall backbone conformation of GA1 appears nearly to be extended with a little bent at the glycosidic II–III linkage, in which two pyranose rings of Gal(IV)-GalNAc-(III) moiety orient approximately perpendicular to those of Gal(II)-Glc(I) moiety. This is consistent with the structures deduced from high-sensitivity differential scanning calorimetry experiments and the nmr study on GA1. The calculated glycosidic torsion angles of the lowest free energy conformation of GA1 in the hydrated state are in accord with the structures of relevant oligosaccharides deduced from nmr experiments and hard sphere exoanomeric calculations. A comparison of the values of glycosidic torsion angles ϕ and π of GA1 and its constituent oligosaccharides indicates that the overall backbone conformation of each oligosaccharide is retained when the oligosaccharide chain becomes longer. This implies that the short-range interactions between the nearest-neighbored saccharides are of significant importance in stabilizing the overall backbone conformation of GA1 in both the unhydrated and hydrated states. The different orientation and hydrogen bonds of hydroxymethyl and hydroxyl groups from one oligosaccharide to another suggest that the medium- and long-range interactions are also of consequence. Hydration seems to affect significantly the conformation of these groups, but not to perturb remarkably the overall backbone conformation of GA1. © 1997 John Wiley & Sons, Inc. Biopoly 42: 19–35, 1997     

Synthesis, crystal structures and density functional theory study of dimeric copper(II) complexes of a tridentate Schiff-base ligand

Oxalate- or 4,4′-bipyridine-bridged dimeric copper(II) complexes, [Cu₂L₂(μ-ox)] (1) and [Cu₂L₂(μ-bipy)](BF₄)₂ (2) [where ox = oxalate, bipy = 4,4′-bipyridine, HL = N-(1H-pyrrol-2-ylmethylene)-2-pyridineethanamine, L⁻ = HL−H⁺], have been synthesised and characterised by elemental analysis, IR, UV-Vis and single crystal X-ray diffraction. Crystal structure determinations carried out on 1 and 2 reveal that 1 is an oxalate-bridged centrosymmetrical square pyramidal dimeric copper(II) complex while 2 is a 4,4′-bipyridine-bridged non-centrosymmetric square planar dinuclear copper(II) complex. Comparison of the optimised geometries with the corresponding crystal structures suggests that the B3LYP/LANL2DZ level can reproduce the structures of 1 and 2 on the whole. The electronic spectra of 1 and 2 predicted by B3LYP/LANL2DZ method show some blue shifts compared with their experimental data. Thermal analysis carried out on 1 shows that there is only one exothermal peak at about 260 °C and the residue is presumably Cu₂O₄N₆.     

Electronic structure study using density functional theory in organic dendrimers

The electronic and structural properties of pyrrolic ring derivatives were studied using density functional theory (DFT) in terms of their application as organic semiconductor materials in photovoltaic devices. The B3LYP hybrid functional in combination with Pople type 6-31G(d) basis set with a polarization function was used in order to determine the optimized geometries and the electronic properties of the ground state, while transition energies and excited state properties were obtained from time-dependent (TD)-DFT with B3LYP/6-31G(d) calculation. The investigation of pyrrolic derivatives formed by the arrangement of several monomeric units revealed that three-dimensional (3D) conjugated architectures in which the combination of a triphenylamine (TPA) core with π-conjugated rings attached to the core, present the best geometric and electronic characteristics for use as an organic semiconductor material. The highest occupied molecular orbital (HOMO) − lowest unoccupied molecular orbital (LUMO) energy gap was decreased in 3D-structures that extend the absorption spectrum toward longer wavelengths, revealing a feasible intramolecular charge transfer process in these systems. All calculations in this work were performed using the Gaussian 03 W software package.     

Hydrogen bonds in galactopyranoside and glucopyranoside: a density functional theory study

Density functional theory calculations on two glycosides, namely, n-octyl-β-D-glucopyranoside (C₈O-β-Glc) and n-octyl-β-D-galactopyranoside (C₈O-β-Gal) were performed for geometry optimization at the B3LYP/6-31G level. Both molecules are stereoisomers (epimers) differing only in the orientation of the hydroxyl group at the C4 position. Thus it is interesting to investigate electronically the effect of the direction (axial/equatorial) of the hydroxyl group at the C4 position. The structure parameters of X-H???Y intramolecular hydrogen bonds were analyzed, while the nature of these bonds and the intramolecular interactions were considered using the atoms in molecules (AIM) approach. Natural bond orbital analysis (NBO) was used to determine bond orders, charge and lone pair electrons on each atom and effective non-bonding interactions. We have also reported electronic energy and dipole moment in gas and solution phases. Further, the electronic properties such as the highest occupied molecular orbital, lowest unoccupied molecular orbital, ionization energy, electron affinity, electronic chemical potential, chemical hardness, softness and electrophilicity index, are also presented here for both C₈O-β-Glc and C₈O-β-Gal. These results show that, while C₈O-β-Glc possess– only one hydrogen bond, C₈O-β-Gal has two intramolecular hydrogen bonds, which further confirms the anomalous stability of the latter in self-assembly phenomena.     

Structure-activity relationship study of flavone compounds with anti-HIV-1 integrase activity: a density functional theory study

Human immunodeficiency virus type-1 integrase (HIV-1 IN) is an essential enzyme for effective viral replication. Flavone compounds have been very much studied due to their activity during the inhibition process of HIV-1 IN. In this study, we employed density functional theory (DFT) using the B3LYP hybrid functional to calculate a set of molecular properties for 32 flavonoid compounds with anti-HIV-1 IN activity. The stepwise discriminant analysis (SDA), principal component analysis (PCA) and hierarchical cluster analysis (HCA) methods were employed to reduce dimensionality and investigate possible relationship between the calculated properties and the anti-HIV-1 IN activity. These analyses showed that the molecular hydrophobicity (ClogP), charge on atom 11 and electrophilic index (omega) are responsible for the separation between anti-HIV-1 IN active and inactive compounds.     

Molecular structure and spectroscopic (FT-IR,FT-Raman, 13C, 1H NMR and UV) studies of 3,4-dihydroxy-l-phenylalanine using density functional theory

Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra of 3,4-dihydroxy-l-phenylalanine (3,4-DPA) in solid phase were recorded and analysed in this research. Along with this, the IR spectra in CHCl₃ and the use of acetone as solvents of 3,4-DPA were also recorded. The equilibrium geometry, bonding features and harmonic vibrational frequencies were investigated with the help of density functional theory (DFT) method. The ¹H and ¹³C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge including atomic orbital method and compared with experimental results. Stability of the molecule arising from hyperconjugative interactions and charge delocalisation was analysed using natural bond orbital analysis. The results show that charge in electron density (E _D) in the σ* and π* antibonding orbitals and second-order delocalisation energies E(2) confirms the occurrence of intramolecular charge transfer within the molecule. UV–vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were analysed using the time-dependent (TD)-DFT approach. Finally, the calculation results were applied to simulate infrared and Raman spectra of the title compound, which showed good agreement with the observed spectra.     

A density functional theory study of the decomposition mechanism of nitroglycerin

The detailed decomposition mechanism of nitroglycerin (NG) in the gas phase was studied by examining reaction pathways using density functional theory (DFT) and canonical variational transition state theory combined with a small-curvature tunneling correction (CVT/SCT). The mechanism of NG autocatalytic decomposition was investigated at the B3LYP/6-31G(d,p) level of theory. Five possible decomposition pathways involving NG were identified and the rate constants for the pathways at temperatures ranging from 200 to 1000 K were calculated using CVT/SCT. There was found to be a lower energy barrier to the β-H abstraction reaction than to the α-H abstraction reaction during the initial step in the autocatalytic decomposition of NG. The decomposition pathways for CHOCOCHONO₂ (a product obtained following the abstraction of three H atoms from NG by NO₂) include O–NO₂ cleavage or isomer production, meaning that the autocatalytic decomposition of NG has two reaction pathways, both of which are exothermic. The rate constants for these two reaction pathways are greater than the rate constants for the three pathways corresponding to unimolecular NG decomposition. The overall process of NG decomposition can be divided into two stages based on the NO₂ concentration, which affects the decomposition products and reactions. In the first stage, the reaction pathway corresponding to O–NO₂ cleavage is the main pathway, but the rates of the two autocatalytic decomposition pathways increase with increasing NO₂ concentration. However, when a threshold NO₂ concentration is reached, the NG decomposition process enters its second stage, with the two pathways for NG autocatalytic decomposition becoming the main and secondary reaction pathways.     

The adsorption of mercury-species on relaxed and rumpled CaO (0 0 1) surfaces investigated by density functional theory

This research examines the importance of several computational choices in modeling mercury species adsorption on calcium oxide surfaces and is the second in a series of papers. The importance of surface relaxation was tested and it was found that adsorption energies changed for HgCl₂, moving adsorption from being at the borderline of physisorption and chemisorption to being strongly chemisorbed. Results for Hg and HgCl were unaffected. A second computational choice, that of the cluster or periodic model size was tested in both the plane of the model (4 × 4 or 5 × 5 model sizes) and for the depth (two or three layers). It was found that the minimum cluster size for handling mercury adsorption was 5 × 5 and that only two layers of depth were needed. The energetic results show that rumpled CaO surfaces will only weakly physisorb elemental mercury, but could be used to capture HgCl₂ from coal combustion flue gases, which is in agreement with limited experimental data.     

Structural, electronic and magnetic effects of Al-doped niobium clusters: a density functional theory study

The application of the ab initio stochastic search procedure with Saunders "kick" method has been carried out for the elucidation of global minimum structures of a series of Al-doped clusters, Nb(n)Al (1 ≤ n ≤ 10). We have studied the structural characters, growth behaviors, electronic and magnetic properties of Nb(n)Al by the density functional theory calculations. Unlike the previous literature reported on Al-doped systems where ground state structures undergo a structural transition from the Al-capped frame to Al-encapsulated structure, we found that Al atom always occupies the surface of Nb(n)Al clusters and structural transition does not take place until n = 10. Note that the fragmentation proceeds preferably by the ejection of an aluminum atom other than niobium atom. According to the natural population analysis, charges always transfer from aluminum to niobium atoms. Furthermore, the magnetic moments of the Nb(n)Al clusters are mainly located on the 4d orbital of niobium atoms, and aluminum atom possesses very small magnetic moments.     

Conformational changes in HIV-1 gp41 in the course of HIV-1 envelope glycoprotein-mediated fusion and inactivation

HIV-1 envelope glycoprotein-mediated fusion is driven by the concerted coalescence of the HIV-1 gp41 N- and C-helical regions, which results in the formation of 6-helix bundles. These two regions are considered prime targets for peptides and antibodies that inhibit HIV-1 entry. However, the parameters that govern this inhibition have yet to be elucidated. We address this issue by monitoring the temporal sequence of conformational states of HIV-1 gp41 during the course of HIV-1-mediated cell-cell fusion by quantitative video microscopy using reagents that bind to N- and C-helical regions, respectively. Env-expressing cells were primed by incubation with target cells at different times at 37 degrees C followed by washing. The reactivity of triggered gp41 to the NC-1 monoclonal antibody, which we demonstrate here to bind to N-helical gp41 trimers, increased rapidly to a maximal level in the primed state but decreased once stable fusion junctions had formed. In contrast, reactivity with 5-helix, which binds to the C-helical region of gp41, increased continuously as a function of time following the priming. The peptide N36(Mut(e,g)) reduced NC-1 monoclonal antibody binding and enhanced 5-helix binding, consistent with the notion that this molecule promotes dissociation of gp41 trimers. This inactivation pathway may be important for the design of entry inhibitors and vaccine candidates.     

OH-functionalized open-ended armchair single-wall carbon nanotubes (SWCNT) studied by density functional theory

The structures of ideal armchair (5,5) single-wall carbon nanotubes (SWCNTs) of different lengths (3.7, 8.8, and 16.0 Å for C₄₀H₂₀, C₈₀H₂₀, and C₁₄₀H₂₀) and with 1–10 hydroxyl groups at the end of the nanotube were fully optimized at the B3LYP/3-21G level, and in some cases at the B3LYP/6-31G* level, and the energy associated with the attachment of the OH substituent was determined. The OH-group attachment energy was compared with the OH functionalization of phenanthrene and picene models and with previous results for zigzag (9.0) SWCNT systems. In comparison to zigzag SWCNTs, the armchair form is more (by about 5 to 10 kcal mol^?1) reactive toward hydroxylation.

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Figure The structures of ideal armchair (5,5) single-wall carbon nanotubes (SWCNTs) of different lengths (3.7, 8.8, and 16.0 Å for C₄₀H₂₀, C₈₀H₂₀, and C₁₄₀H₂₀) and with 1–10 hydroxyl groups at the end of the nanotube were fully optimized at the B3LYP/3-21 G level, and in some cases at the B3LYP/6-31 G* level, and the energy associated with the attachment of the OH substituent was determined.

     

Photodissociation of a ruthenium(II) arene complex and its subsequent interactions with biomolecules: a density functional theory study

The piano-stool Ru(II) arene complex [(η(6)-benz)Ru(bpm)(py)](2+) (benz?=?benzene, bpm?=?2,2'-bipyrimidine, and py?=?pyridine), which is conventionally nonlabile (on a timescale and under conditions relevant for biological reactivity), can be activated by visible light to selectively photodissociate the monodentate ligand (py). In the present study, the aquation and binding of the photocontrolled ruthenium(II) arene complex [(η(6)-benz)Ru(bpm)(py)](2+) to various biomolecules are studied by density functional theory (DFT) and time-dependent DFT (TDDFT). Potential energy curves (PECs) calculated for the Ru-N (py) bonds in [(η(6)-benz)Ru(bpm)(py)](2+) in the singlet and triplet state give useful insights into the photodissociation mechanism of py. The binding energies of the various biomolecules are calculated, which allows the order of binding affinities among the considered nuleic-acid- or protein-binding sites to be discerned. The kinetics for the replacement of water in the aqua complex with biomolecules is also considered, and the results demonstrate that guanine is superior to other biomolecules in terms of coordinating with the Ru(II) aqua adduct, which is in reasonable agreement with experimental observations.