DFT study of glucose based glycolipid crown ethers and their complexes with alkali metal cations Na+ and K+

A theoretical study of a series of five glucose based glycolipid crown ethers and their complexes with Na⁺ and K⁺ was performed using the density functional theory with B3LYP/6-31?G* to obtain the optimized geometrical structures and electronic properties. The local nucleophilicity of the five molecules was investigated using Fukui function, while the global nucleophilicity was calculated from the ionization potential and electron affinity. The structures and coordination of the complexes were studied to identify the best match of the glycolipid crown ethers with cations. In general, it was found that the oxygen atoms pairs O2 and O3 (or O4 and O6) on the sugar ring are constrained from moving toward the cation, which results in a weaker O-cation coordination strength for the oxygen pair compared to the other oxygen atoms in the crown ether ring. The thermodynamic properties of the binding of the complexes and the exchange reaction in gas phase were evaluated. The cation selectivity pattern among the five molecules was in good agreement with the experiment.     

DFT study of new bipyrazole derivatives and their potential activity as corrosion inhibitors

In the present work, a theoretical study of five bipyrazolic-type organic compounds, 4-{bis[(3,5-dimethyl-1H-pyrazolyl-1-yl)methyl]-amino}phenol (1), N1,N1-bis[(3,5-dimethyl-1H-pyrazol-1-yl)methyl}]-N4,N4-dimethyl-1,4-benzenediamine (2), N,N-bis[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]aniline (3), 4-[bis(3,5-dimethyl pyrazol-1-yl-methyl)-amino]butan-1-ol (4) and ethyl4-[bis(3,5-dimethyl-1H-pyrazol-1-yl-methyl) aminobenzoate] (5), has been performed using density functional theory (DFT) at the B3LYP/6-31G(d) level in order to elucidate the different inhibition efficiencies and reactive sites of these compounds as corrosion inhibitors. The efficiencies of corrosion inhibitors and the global chemical reactivity relate to some parameters, such as EHOMO, ELUMO, gap energy (ΔE) and other parameters, including electronegativity (χ), global hardness (η) and the fraction of electrons transferred from the inhibitor molecule to the metallic atom (ΔN). The calculated results are in agreement with the experimental data on the whole. In addition, the local reactivity has been analyzed through the Fukui function and condensed softness indices.     

Tris(pyrazol-1-yl)borate and tris(pyrazol-1-yl)methane: A DFT study of their different binding capability toward Ag(I) and Cu(I) cations

Density functional theory has been used to study the electronic structure of [M(tp)] and [M(tpm)]⁺ conformers (M = Cu, Ag; tp = tris(pyrazol-1-yl)borate anion, tpm = tris(pyrazol-1-yl)methane) and the energetics of their interconversions. Results for the free tp ligand are similar to those of tpm [M. Casarin, D. Forrer, F. Garau, L. Pandolfo, C. Pettinari, A. Vittadini, J. Phys. Chem. A 112 (2008) 6723], indicating an intrinsic instability of the tripodal conformation (κ³-like). This points out that, though frequently observed, the κ³-coordinative mode is unlikely to be directly achieved through the interaction of M(I) with the κ³-like tp/tpm conformer. Analogously to the [M(tpm)]⁺ molecular ions, the energy barrier for the κ²-[M(tp)] → κ³-[M(tp)] conversion is computed to be negligible. Though κⁿ-[M(tp)] and κⁿ-[M(tpm)]⁺ (n = 1, 2, 3) have similar metal-ligand covalent interactions, the negative charge associated to the tp ligand makes the M-tp bonding stronger.     

Determination of the absolute configurations of chiral organometallic complexes via density functional theory calculations of their vibrational circular dichroism spectra: The chiral chromium tricarbonyl complex of N-pivaloyl-tetrahydroquinoline

The racemate of the chiral tricarbonyl-η⁶-arene-chromium(0) complex, tricarbonyl-η⁶-N-pivaloyl-tetrahydroquinoline-chromium(0), 1, has been synthesized and resolved using chromatography on a (R,R)-Whelk-O1 column. The Absolute Configuration (AC) of 1 has been determined using vibrational circular dichroism (VCD) spectroscopy. The VCD spectrum of 1 has been predicted using the Stephens equation for vibrational rotational strengths, implemented using density functional theory (DFT) in the gaussian program. Using the B3PW91 functional and the 6-311++G (2d,2p) basis set, the predicted VCD spectrum of S-1 is in excellent agreement with the experimental VCD spectrum of (+)-1, leading unambiguously to the AC S-(+). It is concluded that VCD is a useful technique for determining the ACs of chiral organometallic complexes, given the use of optimum functionals and basis sets.     

The ground-state Na+ affinities of a series of substituted acetophenones: a DFT study

A detailed study of Na⁺ affinities of a series of para-substituted acetophenones and their O–Na⁺ counterparts was performed using density functional theory [Becke, Lee, Yang and Parr (B3LYP)] method using 6-311G(d,p) basis sets with complete geometry optimisation. The gas-phase O–Na⁺ complex formation turns out to be an exothermic case and the local stereochemical disposition of Na⁺ is found to be almost the same in each case. The presence of the para-substituent is seen to cause very little change in the Na⁺ affinity relative to the unsubstituted acetophenones. Electron-releasing p-substituents increase it by 0.0105 hartree and electron-withdrawing p-substituents decrease it by 0.011 hartree. Computed Na⁺ affinities are sought to be correlated with a number of computed system parameters such as the net charge on the Na⁺ and the carbonyl oxygen of the Na⁺ complexes and the net charge on the carbonyl oxygen of the free bases. The energetics, structural and electronic properties of the complexes indicate that the interaction between the Na⁺ ion and a carbonyl base is predominantly an ion–dipole attraction and the ion-induced dipole interaction as well rather than a covalent interaction.     

DFT studies of the electronic structure and geometry of 18-crown-6, hexaaza[18]annulene, and their complexes with cations of the heavier alkali and alkaline earth metals

DFT calculations for M@C₁₂H₁₂N₆ and M@C₁₂H₂₄O₆ (where M = Rb⁺, Cs⁺, Sr²⁺, and Ba²⁺, C₁₂H₁₂N₆ = hexaaza[18]annulene, and C₁₂H₂₄O₆ = 18-crown-6) were performed using the recently developed model core potential parametrization. Results show that the ions bind more strongly to C₁₂H₁₂N₆ than to 18-crown-6 moiety; the difference is more pronounced for cations with smaller radii.     

Theoretical study on the thermal decomposition of model compounds for Poly (dialkyl fumarate)

The thermal decomposition of model compounds for poly (dialkyl fumarate) was studied by using ab initio and density functional theory (DFT) calculations. To determine the most favorable reaction pathway of thermal decomposition, geometries, structures, and energies were evaluated for reactants, products, and transition states of the proposed pathways at the HF/6-31G(d) and B3LYP/6-31G(d) levels. Three possible paths (I, II and III) and subsequent reaction paths (IV and V) for the model compounds of poly (dialkyl fumarate) decomposition had been postulated. It has been found that the path (I) has the lowest activation energy 193.8 kJ mol⁻¹ at B3LYP/6-31G(d) level and the path (I) is considered as the main path for the thermal decomposition of model compounds for poly (dialkyl fumarate).      

One and two dimensional 1H and 13C high resolution NMR investigation of lariat ethers and their alkali metal ionic complexes: a more tangible evidence for the presence of less common C-H***O hydrogen bonds

The possible existence of less common hydrogen bonds in three lariat ethers and their alkali-metal ionic complexes have been investigated with one- and two-dimensional (1D and 2D) proton and carbon-13 high resolution liquid state NMR spectroscopy. The occurrence of hydrogen-bonding induced by the addition of metal ions has been identified with the observation of indirect dipolar coupling between the coupling partners involved in the hydrogen-bonding. The addition of metal ions, moreover, causes appreciable change of chemical shift of several protons and carbons. The chemical shift change depends on the ion radius, larger ions causing smaller change. Moreover, the change of chemical shift is in coincidence with the occurrence of hydrogen-bonding. The values of the coupling constants have been obtained for each of these hydrogen bonds and were used for evaluating the hydrogen-bond strength. An intriguing and surprising observation is that a C-H***O hydrogen bond identified in solution by this work was not found in the previous study with X-ray diffraction or other methods.     

DFT: a dynamic study of the interaction of ethanol and methanol with platinum

The interaction between alcohol molecules and platinum (Pt) was studied using molecular dynamics (MD; Born-Oppenheimer method). Alcohol molecules like ethanol and methanol present a similar molecular structure, with a methyl group (CH₃) at one end and a fragment of hydroxyl (OH) at the other. This fact generates two orientations that are considered in the interaction with Pt. The MD calculation results for these two orientations indicate a preferential orientation due to energy interactions. A plausible reaction mechanism that takes into account the interaction between Pt and alcohol is presented. The charge transference obtained from the Pt–alcohol interaction was also analyzed. The energy for the two orientations was calculated by indicating the preferential orientation. The methyl and hydroxyl groups are involved in heterolytic breakage of hydrogen bonds, joined to a carbon atom in the former and to an oxygen atom in the latter; however, the methyl group reaction seems to be the most important.     

DFT study of the intrinsic conformations of [2Fe-2S-4(SCH3)] clusters and their influence on exchange coupling

We have determined the equilibrium conformations of the diiron(III) cluster [2Fe-2S-4(SCH₃)]²⁻ using density functional theory. The conformers have dihedral Fe-Fe-S-C angles of ∼0° and ±120°. The relative energies of the conformers can be accurately parameterized with a small number of side-chain repulsion parameters. Of the 17 conformers identified on the basis of the ideal values for the dihedrals, 10 conformers are stable in both the ferromagnetic and broken symmetry state for the cluster. The exchange coupling constants for the seven energetically lowest conformers are predicted to belong to a narrow range, 150 cm⁻¹ ? J ? 178 cm⁻¹. The cluster conformers found in proteins do not coincide with any of the intrinsic ones, due to distortion of one of the dihedral angles under the influence of the protein scaffold.     

Compounds of the 1,5-di(4-R-phenyl)-3-selenopentanediones-1,5 series interaction with the Basidiomycete Lentinula edodes,lectins: Computations and Experiment

Abstract

The role of spatial and electron structure, hydrophobic properties and concentration of organoselenium compounds on their interaction with fungal metabolites - extracellular lectins of Lentinula edodes, (shiitake mushroom) has been considered. By the hybrid method of density functional theory at the B3LYP/6-31G(d,p) theory level, spatial and electronic structure of the 1,5-diphenyl-3-selenopentanedione-1,5 (preparation DAPS-25), 1,5-di(4-methoxyphenyl)-3-selenopentanedione-1,5 and 1,5-di(4-ethoxyphenyl)-3-seleno- pentanedione-1,5 molecules has been studied. The above molecules have been stated to be substantially similar to each other by their electronic and spatial characteristics. By means of the QSAR properties evaluation by the atomic-additive schemes, it has been shown that the molecules of the preparation DAPS-25, its dimethoxy- and diethoxy-substituted are close to each other by the hydrophilic-lipophilic balance, whereas di-n,-octoxy derivative DAPS-25 is explicitly hydrophobic. The hemagglutinating activity of lectins in the presence of the preparation DAPS-25 and its alkyloxy-substituted increases, therewith the most effective addition is 1,5-di(4-ethoxyphenyl)-3-selenopentanedione-1,5. Apparently, the greater effectiveness of the said substance compared to DAPS ?25 is caused by the formation of hydrogen bonds with a participation of unshared electron pairs of oxygen atoms from the ethoxy groups and mobile hydrogen atoms from the OH groups of glycoconjugates on erythrocytes surface. The positive effect of 1,5-di(4-n-octoxyphenyl)-3-selenopentanedione-1,5 is not so prominent, since the enlarged alkyl chain shields the aromatic fragments of organoselenium molecule participating in the binding with lectin.     

Theoretical study of 1-(4-hexylcyclohexyl)-4-isothiocyanatobenzene: molecular properties and spectral characteristics

The mesogenic species 4-(4-hexylcyclohexyl) isothiocyanatobenzene (6CHBT) was studied with density functional theory and molecular mechanics in order to investigate the molecular properties, interactions between dimers and to interpret the IR spectrum. Two types of calculations were performed for model systems containing single and double molecules of 6CHBT. Calculations (involving conformation analysis) for isolated species indicated that the trans isomer, in the equatorial–equatorial conformation, is the most energetically stable. The 6CHBT molecule is polar, with a rather high (4.43 D) dipole moment with negatively charged isothiocyanato (NCS) ligand. The dimer–dimer interaction energies show that the head-to-head configuration (where van der Waals attraction forces play the major role) is the most energetically stable. Vibrational analysis provided detailed assignment of the experimental infra-red (IR) spectrum. Figure Most favorite 6CHBT head to head interaction - ESP mapped to electron density surface Dedication  This paper is dedicated to the memory of Dr. Wacław Witko, who introduced us to research on mesogenic systems.     

The Impact of Model Peptides on Structural and Dynamic Properties of Egg Yolk Lecithin Liposomes – Experimental and DFT Studies

Electron spin resonance (ESR), ¹H‐NMR, voltage and resistance experiments were performed to explore structural and dynamic changes of Egg Yolk Lecithin (EYL) bilayer upon addition of model peptides. Two of them are phenylalanine (Phe) derivatives, Ac‐Phe‐NHMe ( 1 ) and Ac‐Phe‐NMe₂ ( 2 ), and the third one, Ac‐(Z)‐ΔPhe‐NMe₂ ( 3 ), is a derivative of (Z)‐α,β‐dehydrophenylalanine. The ESR results revealed that all compounds reduced the fluidity of liposome's membrane, and the highest activity was observed for compound 2 with N‐methylated C‐terminal amide bond (Ac‐Phe‐NMe₂). This compound, being the most hydrophobic, penetrates easily through biological membranes. This was also observed in voltage and resistance studies. ¹H‐NMR studies provided a sound evidence on H‐bond interactions between the studied diamides and lecithin polar head. The most significant changes in H‐atom chemical shifts and spin‐lattice relaxation times T₁ were observed for compound 1 . Our experimental studies were supported by theoretical calculations. Complexes EYL? Ac‐Phe‐NMe₂ and EYL? Ac‐(Z)‐ΔPhe‐NMe₂, stabilized by NH???O or/and CH???O H‐bonds were created and optimized at M06‐2X/6‐31G(d) level of theory in vacuo and in H₂O environment. According to our molecular‐modeling studies, the most probable lecithin site of H‐bond interaction with studied diamides is the negatively charged O‐atom in phosphate group which acts as H‐atom acceptor. Moreover, the highest binding energy to hydrocarbon chains were observed in the case of Ac‐Phe‐NMe₂ ( 2 ).     

Structural properties of sH hydrate: a DFT study of anisotropy and equation of state

ABSTRACT

Structure-H (sH) hydrate is one of the canonical gas hydrates with significant potential applications and scarce characterised material properties despite the wide knowledge available on other gas hydrates. In this work we characterise some of the important physical properties of this hydrate at the atomistic level using Density Functional Theory. Two exchange-correlation functionals (revPBE and DRSLL) were used to simulate six sH hydrate systems encapsulating neohexane and different help gas molecules. The important role of dispersion forces is quantified. The density and isothermal bulk modulus of sH hydrate are higher when dispersion interactions are considered. The presence of those interactions imposes a direct relationship between the hydrate density and its bulk modulus, while their absence reveals the bulk modulus dependency on hydrogen bond density. Anisotropy is a distinguishing feature of this hydrate in distinction to nearly isotropic sI and sII hydrates. Structure-H hydrate experiences a compressional anisotropy in which the a-lattice and the c-lattice constants respond differently to applied pressure showing less compressibility along the c-axis. This compressional anisotropy was found dependant on the chemistry of help gas molecules. Taken together, these property characterisation results and analysis are a significant and novel contribution to the material physics of sH hydrates.     

Application of bioisosterism in design of the semicarbazone derivatives as cruzain inhibitors: a theoretical and experimental study

A series of semicarbazone, thiosemicarbazone, and aminoguanidine derivatives were synthesized and tested as antitrypanosomal agents. The theoretical NMR of the compounds was calculated using molecular modeling techniques (density functional theory (DFT) calculations) and confirmed the formation of the compounds. The ability to inhibit cruzain and Trypanosoma cruzi epimastigote replication was evaluated. Cruzain inhibition ranged between 70 and 75% (100 μM), and IC₅₀ values observed in epimastigote forms of T. cruzi ranged from 20 to 140 μM. Furthermore, the compounds did not present cytotoxicity at concentrations up to 50 and 250 μM in MTT tests. Molecular modeling studies were conducted using DFT method (B3LYP functional and the basis set 6-311G(d,p)) to understand the activity of the compounds, corroborating the observed cruzain inhibitory activity. In docking studies, the obtained analogs showed good complementarity with cruzain active site. In addition, docking results are in accordance with the susceptibility of these analogs to nucleophilic attack of the catalytic Cys25. Taken together, this study shows that this class of compounds can be used as a prototype in the identification of new antichagasic drugs.     

Ab initio prediction of optical rotation: comparison of density functional theory and Hartree-Fock methods for three 2,7,8-trioxabicyclo[3.2.1]octanes

We report ab initio calculations of the frequency-dependent electric dipole-magnetic dipole polarizabilities, beta(nu), at the sodium D line frequency and, thence, of the specific rotations, [alpha](D), of 2,7,8-trioxabicyclo[3.2.1]octane, 1, and its 1-methyl derivative, 2, using the Density Functional Theory (DFT) and Hartree-Fock/Self-Consistent Field (HF/SCF) methodologies. Gauge-invariant (including) atomic orbitals (GIAOs) are used to ensure origin-independent [alpha](D) values. Using large basis sets which include diffuse functions DFT [alpha](D) values are in good agreement with experimental values (175.8 degrees and 139.2 degrees for (1S,5R)-1 and -2, respectively); errors are in the range 25-35 degrees. HF/SCF [alpha](D) values, in contrast, are much less accurate; errors are in the range 75-95 degrees. The use of small basis sets which do not include diffuse functions substantially lowers the accuracy of predicted [alpha](D) values, as does the use of the static limit approximation: beta(nu) approximately beta(o). The use of magnetic-field-independent atomic orbitals, FIAOs, instead of GIAOs, leads to origin-dependent, and therefore nonphysical, [alpha](D) values. We also report DFT calculations of [alpha](D) for the 1-phenyl derivative of 1, 3. DFT calculations find two stable conformations, differing in the orientation of the phenyl group, of very similar energy, and separated by low barriers. Values of [alpha](D) predicted using two different algorithms for averaging over phenyl group orientations are in good agreement with experiment. In principle, the absolute configuration (AC) of a chiral molecule can be assigned by comparison of the optical rotation predicted ab initio to the experimental value. Our results demonstrate the critical importance of the choice of ab initio methodology in obtaining reliable optical rotations and, hence, ACs, and show that, at the present time, DFT constitutes the method of choice.     

The interactions of square platinum(II) complexes with guanine and adenine: a quantum-chemical ab initio study of metalated tautomeric forms

The influence of binding of square planar platinum complexes on tautomeric equilibria of the DNA bases guanine and adenine was investigated using the density functional B3LYP method. Neutral trans-dichloro(amine)-, +1 charged chloro(diamine)-, and +2 charged triamine-platinum(II) species were chosen for coordination to bases. Only the N₇ interaction site of the bases was considered. The calculations demonstrate that the neutral platinum adduct does not change the tautomeric equilibria of the bases. Furthermore, N₇ binding of the neutral Pt adduct moderately reduces the probability of protonation of the N₁ position of adenine. Larger effects can be observed for +1 and mainly +2 adducts, but these can be rationalized by electrostatic effects. Since the electrostatic effects are expected to be efficiently compensated for by a charged backbone of DNA and counterions in a polar solvent, no dramatic increase in mispair formation is predicted for Pt(II) adducts, which is in agreement with experiment. The interaction energies between Pt adducts and the nucleobases were also evaluated. These interaction energies range from ca. 210 kJ/mol for neutral adducts, interacting with both bases and their tautomers, up to 500 kJ/mol for the +2 charged adducts, interacting with the keto-guanine tautomer and the anti-imino-adenine tautomer. The surprisingly large interaction energy for the latter structure is due to the strong H-bond between the NH₃ ligand group of the metal adduct and the N₆ nitrogen atom of the base. Received: 6 July 1999 / Accepted: 7 December 1999     

Oxidation of diiron and triiron sulfurdithiolato complexes: mimics for the active site of [FeFe]-hydrogenase

The oxidation of the hexacarbonyl(1,3-dithiolato-S,S')diiron complexes 4a-4c with varying amounts of dimethyldioxirane (DMD) was systematically studied. The chemoselectivity of the oxidation products depended upon the substituent R (R=H, Me, 1/2 (CH2)(5)). For R=H, four oxidation products, 6a-6d, have been obtained. In the case of R=Me, three products, 7a-7c, were formed, and for R=1/2 (CH2)(5), only complex 8 was observed. These observations are due to steric and electronic effects caused by the substituent R. Additionally, oxidation of the triiron complex 5 with DMD was performed to yield the products 9a and 9b. X-Ray diffraction analyses were performed for 6a-6d, 7a, and 7c, as well as for 9a and 9b. The electronic properties were determined by density-functional theory (DFT) calculations.     

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.