Electronic and vibrational circular dichroism of aromatic amino acids by density functional theory

Structures of model compounds mimicking aromatic amino acid residues in proteins are optimized by density functional theory (DFT), assuming that the main-chain conformation was a random coil. Excitation energies and dipole and rotational strengths for the optimized structures were calculated based on time-dependent DFT (TD-DFT). The electronic circular dichroism (ECD) bands of the models were significantly affected by side-chain conformations. Hydration models of the aromatic residues were also subjected to TD-DFT calculations, and the ECD bands of these models were found to be highly perturbed by the hydration of the main-chain amide groups. In addition to calculating the random-coil conformation, we also performed TD-DFT calculations of the aromatic residue models, assuming that the main-chain conformation was an alpha-helix or beta-strand. As expected, the overall feature of the ECD bands was also perturbed by the main-chain conformations. Moreover, vibrational circular dichroism (VCD) spectra of the hydration models in a random-coil structure were simulated by DFT, which showed that the VCD spectra are more sensitive to the side-chain conformations than the ECD spectra. The present results show that analyses combining ECD and VCD spectroscopy and using DFT calculations can elucidate the main- and side-chain conformations of aromatic residues in proteins.     

Conformational study of palindromic tripeptides (GPG, IPI and KPK) in HIV-1 protease--a density functional theory study

A comparative study has been carried out on three palindromic tripeptides Gly-Pro-Gly, Ile-Pro-Ile and Lys-Pro-Lys which were present in HIV protein along with their analogues applying density functional computation at B3LYP/6-31G* level of theory. Discrepancy from the structural analysis has been noted for all the systems and it was found to be more for amide capped structure at the C terminal of proline. The puckering amplitude A and Phase angle P of the pyrrolidine ring of proline in the chosen palindromic tripeptides and their analogues were calculated from the endocyclic torsion angles. The minimum energy conformers lying well within the prescribed region of proline were obtained for the derived compounds from potential energy surface scan mentioning that no role has been played by its terminal residues. This is further supported by the simulated amide bands identifying the helical structure for all three palindromic tripeptides signifying the importance of proline. The molecular properties such as stabilization energy, chemical hardness along with dipole moment were calculated and interpreted. The values of Calpha-H(s) and the peptide backbone N-Calpha-CO for all the selected conformers specify the three palindromic tripeptides to have a symmetrical achiral structure.     

High-spin binuclear cyclopentadienyliron chlorides: a density functional theory study

Theoretical studies on the cyclopentadienyliron chlorides Cp₂Fe₂Cl _n (n?=?6???1) with iron in the formal oxidation states from +1 to +4 indicate that all the high-spin species are predicted to be the lowest energy structures and they are paramagnetic complexes with magnetic moments between 2.8μ _B and 5.9μ _B. The mixed oxidation state derivatives with odd number of chloride atoms have larger magnetic moments than other species. In addition to Cp₂Fe₂Cl, which has the largest magnetic moment, these high-spin species have terminal Cp rings and bridging Cl atoms up to a maximum of two bridges. The Cp₂Fe₂Cl₄, Cp₂Fe₂Cl₃ and Cp₂Fe₂Cl₂ derivatives are predicted to be thermodynamically stable molecules with respect to exothermic reactions for the loss of one Cl atom from Cp₂Fe₂Cl _n . Moreover, the lowest energy Cp₂Fe₂Cl _n (n?=?3, 4) derivatives can be derived by the oxidative addition reactions of Cp₂Fe₂Cl _n?2 + Cl₂ → Cp₂Fe₂Cl _n .

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.     

Acetylene chain reaction on hydrogenated boron nitride monolayers: a density functional theory study

Spin-polarized first-principles total-energy calculations have been performed to investigate the possible chain reaction of acetylene molecules mediated by hydrogen abstraction on hydrogenated hexagonal boron nitride monolayers. Calculations have been done within the periodic density functional theory (DFT), employing the PBE exchange correlation potential, with van der Waals corrections (vdW-DF). Reactions at two different sites have been considered: hydrogen vacancies on top of boron and on top of nitrogen atoms. As previously calculated, at the intermediate state of the reaction, when the acetylene molecule is attached to the surface, the adsorption energy is of the order of ?0.82 eV and ?0.20 eV (measured with respect to the energy of the non interacting molecule-substrate system) for adsorption on top of boron and nitrogen atoms, respectively. After the hydrogen abstraction takes place, the system gains additional energy, resulting in adsorption energies of ?1.52 eV and ?1.30 eV, respectively. These results suggest that the chain reaction is energetically favorable. The calculated minimum energy path (MEP) for hydrogen abstraction shows very small energy barriers of the order of 5 meV and 22 meV for the reaction on top of boron and nitrogen atoms, respectively. Finally, the density of states (DOS) evolution study helps to understand the chain reaction mechanism.

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Graphical abstract Acetylene chain reaction on hydrogenated boron nitride monolayers

     

Intramolecular cyclization of isothiocyanyl amino acids/peptide: arrival at unnatural thioxoimidazolidinyl/thioxooxazolidinyl amino acids

Amino Acids - A novel intramolecular cyclization of isothiocyanyl amino acids/peptide is reported to arrive at unnatural thioxoimidazolidinyl (TOI)/thioxooxazolidinyl (TOO) amino acids for the...     

Adsorption of Mn atom on pristine and defected graphene: a density functional theory study

The functionalization of graphene with transition metals is of great interest due to its wide range of applications, such as hydrogen storage, spintronics, information storage, etc. Due to its magnetic property adsorption of Mn atom on graphene has a high consequence on the electronic properties of graphene. The increase in size of the graphene sheet with hydrogen termination has a high impact on the transformation of electronic properties of the graphene sheet. Hence in this work, we investigate the size as well as change in structural and electronic properties of pristine/defective graphene sheets on adsorption of Mn atom using density functional theory methods. From the results obtained a higher adsorption energy value of 3.04 eV is found for Mn adatom on the defected graphene sheet than the pristine, 1.85 eV. It is subject to the coverage effect which decreases on increasing number of carbon atoms. Moreover, a decrease in energy gap is observed in pristine and defected graphene sheets with a high number of carbon atoms. The density of states illustrates the significant effect for hydrogen termination in the conduction band of the Mn adsorbed graphene sheet with low carbon atoms.

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Graphical Abstract Mn adatom on graphene at different sites

     

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.     

The reaction mechanism of phenylethanolamine N-methyltransferase: A density functional theory study

Hybrid density functional theory methods were used to investigate the reaction mechanism of human phenylethanolamine N-methyltransferase (hPNMT). This enzyme catalyzes the S-adenosyl-l-methionine-dependent conversion of norepinephrine to epinephrine, which constitutes the terminal step in the catecholamine biosynthesis. Several models of the active site were constructed based on the X-ray structure. Geometries of the stationary points along the reaction path were optimized and the reaction barrier and energy were calculated and compared to the experimental values. The calculations demonstrate that the reaction takes place via an S_N2 mechanism with methyl transfer being rate-limiting, a suggestion supported by mutagenesis studies. Optimal agreement with experimental data is reached using a model in which both active site glutamates are protonated. Overall, the mechanism of hPNMT is more similar to those of catechol O-methyltransferase and glycine N-methyltransferase than to that of guanidinoacetate N-methyltransferase in which methyl transfer is coupled to proton transfer.     

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.     

A density functional theory study on oxygen reduction reaction on nitrogen-doped graphene

Nitrogen (N)-doped carbons reportedly exhibit good electrocatalytic activity for the oxygen reduction reaction (ORR) of fuel cells. This work provides theoretical insights into the ORR mechanism of N-doped graphene by using density functional theory calculations. All possible reaction pathways were investigated, and the transition state of each elementary step was identified. The results showed that OOH reduction was easier than O–OH breaking. OOH reduction followed a direct Eley–Rideal mechanism (the OOH species was in gas phase, but H was chemisorbed on the surface) with a significantly low reaction barrier of 0.09 eV. Pathways for both four-electron and two-electron reductions were possible. The rate-determining step of the two-electron pathway was the reduction of O₂ (formation of OOH), whereas that of the four-electron pathway was the reduction of OH into H₂O. After comparing the barriers of the rate-determining steps of the two pathways, we found that the two-electron pathway was more energetically favored than the four-electron pathway.     

Exchange interactions in a Fe5 complex: A theoretical study using density functional theory

Theoretical methods based on density functional theory have been employed to analyze the exchange interactions in an Fe₅ complex. The calculated exchange coupling constants are consistent with an S = 15/2 ground state and agree well with those reported previously for other Fe^III polynuclear complexes. The strongest antiferromagnetic interactions are those through a double oxo-benzotriazole bridging ligand, where the benzotriazole ligand seems to play a minor role and the exchange coupling constants present values typical of single oxo bridging systems.     

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。     

Effect of microsolvation on zwitterionic glycine: an ab initio and density functional theory study

The effect of microsolvation on zwitterionic glycine, considering both (-NH3(+)) as proton donor and (-COO(-)) as proton acceptor at correlated ab initio (MP2) level and density functional methods (B3LYP, PW91, MPW1PW91 and PBE) using 6-311++G** basis set has been reported. DFT methods have been employed so as to compare the performance/quality of different gradient-corrected correlation functionals (PW91, PBE), hybrid functionals (B3LYP, MPW1PW91) and to predict the near quantitative structural and vibrational properties, at reduced computational cost. B3LYP method outperforms among the different DFT methods for the computed hydrogen bond distances and found closer to the value obtained by correlated MP2 level, whereas MPW1PW91 and PBE methods shows very similar values but approximately 0.03 A less, compared to B3LYP method. MP2 calculation and single point CCSD(T)//MP2 calculation have been considered to decompose the interaction energy, including corrections for basis set superposition error (BSSE). Moreover, charge distribution analysis has also been carried out to understand the long raised questions, how and why the two body energies have significant contribution to the total binding energy.     

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.     

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.