Application of standard DFT theory for nonbonded interactions in soft matter: prototype study of poly-para-phenylene

We present a detailed analysis of the application of density functional theory (DFT) methods to the study of structural properties of molecular and supramolecular systems, using as a paradigmatic example three para-phenylene-based systems: isolated biphenyl, single chain poly-para-phenylene, and crystalline biphenyl. We use different functionals for the exchange correlation potential, the local density (LDA), and generalized gradient approximations (GGA), and also different basis sets expansions, localized, plane waves (PW), and mixed (localized plus PW), within the reciprocal space formulation for the hamiltonian. We find that regardless of the choice of basis functions, the GGA calculations yield larger interring distances and torsion angles than LDA. For the same XC approximation, the agreement between calculations with different basis functions lies within 1% (LDA) or 0.5% (GGA) for distances, and while PW and mixed basis calculations agree within 1 degrees for torsion angles, the localized basis results show larger angles by approximately 8 degrees and a nonmonotonic dependence on basis size, with differences within 6 degrees. The most prominent features, namely the torsion between rings for isolated molecule and infinite chain, and planarity for the molecule in crystalline environment, are well reproduced by all DFT calculations.     

A DFT study of H-isomerisation in alkoxy-, alkylperoxy- and alkyl radicals: Some implications for radical chain reactions in polymer systems

Intramolecular 1-n H-shift (n = 2, 3… 7) reactions in alkoxy, alkyl and peroxy radicals were studied by density functional theory (DFT) at the B3LYP/6-311+G∗∗ level and compared with respective intermolecular H-transfers. It was found that starting from 1 to 3 H-shift the barrier heights stepwise decrease with increasing n reaching minimum for 1-5 and 1-6 H-shifts. This dependence can be ascribed to the decrease of the strain with increasing transition state (TS) ring size, which is minimal in six- and seven-member rings. The barrier heights of H-shifts in alkyl radicals are systematically larger than those in alkoxy radicals: the respective activation energies (E_a) of 1-5 and 1-6 H-shifts are about 59-67 kJ/mol for alkyl radical and 21-34 kJ/mol for alkoxy radicals. Further increase of the TS ring size in 1-7 H-shifts leads to the increase of the barrier to 44 kJ/mol in the hexyloxy radical and 84 kJ/mol for n-heptyl radical. We have also found that intermolecular H-transfer reactions in all three types of free radicals have smaller barriers than respective intramolecular 1-5 or 1-6 H-shifts by 4-25 kJ/mol. The mentioned difference can be explained in terms of enhanced nonbonding repulsion interaction in the cyclic TS structures compared to respective intermolecular TS. B3LYP/6-311+G∗∗ geometric parameters and imaginary frequencies for 1-n H-shifts TS are consistent with respective calculated barrier heights. Reactivity of some other radicals compared to alkoxy, peroxy and alkyl radicals as well as other factors influencing their reactivity (π-conjugation, steric effect and ring strain in cyclic TS, etc.) are also briefly discussed in relation to free radical reactions in polymer systems.     

Impact of divalent metal cations on the catalysis of peptide bonds: a DFT study

Within the ATP-grasp family of enzymes, divalent alkaline earth metals are proposed to chelate terminal ATP phosphates and facilitate the formation of peptide bonds. Density functional theory methods are used to explore the impact of metal ions on peptide bond formation, providing an insight into experimental metal substitution studies. Calculations show that alkaline earth and transition metal cations coordinate with an acylphosphate reactant and aid in the separation of the phosphate leaving group. The critical biochemical reaction is proposed to proceed through the formation of a six-membered transition state in the relatively nonpolar active site of human glutathione synthetase, an ATP-grasp enzyme. While the identity of the metal ion has a moderate impact on the thermodynamics of peptide bond formation, kinetic differences are much sharper. Simulations indicate that several transition metal ions, most notably Cu²⁺, may be particularly advantageous for catalysis. The detailed mechanistic study serves to elucidate the vital role of coordination chemistry in the formation of peptide bonds.     

Influence of the H/F replacement on the homoaromaticity of homotropylium ion: a GIAO/DFT theoretical study

The problem of homoaromaticity in mono-, di- and polyfluorinated- homotropylium cations is addressed by the B3LYP/6-311++G** DFT method. The energetic, structural and magnetic criteria are used for this purpose. They convincingly show that the ground state equilibrium species are aromatic, or in other words that the homoaromaticity is preserved by the (poly)fluorination. In contrast, a considerable decrease in the aromatic stabilization is observed in the transition structures (TS). According to the NICS(0) index, they vary form strongly antiaromatic, via weakly and non-aromatic to slightly aromatic transition states. However, the hierarchy of the aromaticity in fluorinated homotropylium ions predicted by NICS(0) is completely unrelated to that obtained by using the energy criterion assuming a kinetic definition of aromaticity. On the other hand the latter is closely related to geometric parameters of the equilibrium and transition structures.     

Atoms-in-molecules analysis for planewave DFT calculations--a numerical approach on a successively interpolated charge density grid

We used a successive charge interpolation scheme and Ridders method for differentiation, to acquire accurate charge densities and their higher derivatives in electronic structure calculations. This enables us to search bond critical points using arbitrary charge density grids. We applied the planewave-DFT code, VASP, to generate the charge density of selected benchmark molecules. The properties of bond critical points are in good agreement with those obtained by complementary implementations. We validated our GRID implementation by performing electronic structure calculations using the Gaussian 03 program package and various tools for analysis of the charge density provided by the AIMPAC package. In particular, we carefully investigate the influence of effective core potentials on the location of bond critical points, especially for a short chemical bond, which is crucial in the present pseudopotential-based planewave DFT calculations. We expect our generic implementation will not only be useful for the analysis of chemical bonding in molecules, but will particularly provide a microscopic understanding of extended systems including periodic boundary conditions.     

Effect of GTP and GDP nucleotides on vinblastine binding affinity to tubulin: a DFT study

Vinblastine (VLB) is an anticancer agent that inhibits microtubule assembly by binding with tubulin. Density functional theory (DFT) calculations are used to examine low-energy minima of the energy surface of vinblastine-tubulin complex. Thermodynamic data of the binding site of vinblastine to tubulin are extracted with the hybrid DFT (B3LYP (Becke, three-parameter, Lee–Yang–Parr)) method, and then the influence of several solvents, such as water, methanol and ethanol, and different temperatures are discussed on infrared parameters by self-consistent reaction field (SCRF = dipole) method. The effect of guanosine triphosphate (GTP) and guanosine diphosphate (GDP) nucleotides on vinblastine binding affinity to tubulin was realised in water solvent by comparing the changes of ?G (Gibbs free energy) of VLB-tubulin and VLB-tubulin bonded to GTP or GDP. The result showed that GDP and GTP increase significantly the binding affinity and the role of GDP is more important than that of GTP.     

A new massively parallel version of CRYSTAL for large systems on high performance computing architectures

Fully ab initio treatment of complex solid systems needs computational software which is able to efficiently take advantage of the growing power of high performance computing (HPC) architectures. Recent improvements in CRYSTAL, a periodic ab initio code that uses a Gaussian basis set, allows treatment of very large unit cells for crystalline systems on HPC architectures with high parallel efficiency in terms of running time and memory requirements. The latter is a crucial point, due to the trend toward architectures relying on a very high number of cores with associated relatively low memory availability. An exhaustive performance analysis shows that density functional calculations, based on a hybrid functional, of low‐symmetry systems containing up to 100,000 atomic orbitals and 8000 atoms are feasible on the most advanced HPC architectures available to European researchers today, using thousands of processors. © 2012 Wiley Periodicals, Inc.     

Ring opening of boriranes vis‐à‐vis aziridines: An ab initio and DFT probe on the mechanisms

Borirane undergoes ring opening reaction with NOCl and HNF₂ yielding the corresponding alkenes. Ab initio and density functional investigations of this reaction with cis‐ and trans‐2,3‐dimethylboriranes reveal that these reactions take place in a single step through the formation of a prereactive complex and a transition state giving the alkene with the same stereochemistry. Calculations clearly show that the concerted cleavage of C? B bonds leads to retention of stereochemistry. Further, it shows that HNF₂ cleaves boriranes more efficiently than does NOCl. Intrinsic reaction coordinate analyses and bond order analysis describe the nature of the transition state very well and fix the reaction mechanism. Solvent effect calculations through PCM model, with acetonitrile and CCl₄ as solvents, do not alter the gas phase results significantly. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Assessing a double silicon decorated fullerene for the delivery of interacting flurbiprofen and salicylic acid drugs: A DFT approach

Since the number of drugs increases constantly, drug interactions appear as a critical issue to handle. The effective use of multiple drugs appears as another important subject to discuss and the use of targeted and selective delivery of drugs is becoming more important. Impurity doped C₆₀ fullerenes with various dopant atoms such as silicon or boron appear as promising drug delivery vehicles. Therefore, in the framework of this study, we investigated the interaction between salicylic acid and flurbiprofen and their controlled delivery by using double silicon decorated C₆₀ fullerene using density functional theory. Stability and reactivity considerations were also examined by investigating some important structural parameters, interaction energies and frontier molecular orbitals. The interactions were also monitored by examining important diagnostic vibrational bands. The strength of the interactions between atoms at the interaction sites was also identified by using the quantum theory of atoms in molecules.     

The adsorption of CaOH+ on (001) basal and (010) edge surface of Na‐montmorillonite: a DFT study

Ca²⁺ cations were generally added to facilitate the coagulation of stable fine clay mineral dispersion due to the specific adsorption of their first hydrolysis CaOH⁺ species at pH near 10. The adsorption of CaOH⁺ on dry and hydrated (001) basal surface and (010) surface of Na‐montmorillonite was investigated by using density functional theory method combined with the periodic slab model method. The adsorption energies and geometries, Mulliken charge, electron density difference, and density of state were presented and discussed. It was found that the adsorption energy of CaOH⁺ on (010) edge surface of Na‐montmorillonite (?328.8 kJ/mol) was much larger than that (?126.9 kJ/mol) on (001) basal surface. The presence of waters could increase the adsorption energy of CaOH⁺ on (001) surface but affect that on (010) surface slightly. The protons in Si–OH and Al–OH₂ groups as well as the OH₂ ligands in Al–OH₂ group on (010) edge surface were easily dissociated and coordinated to CaOH⁺ to form new waters. CaOH⁺ was the most steady adsorption species among CaOH⁺, Ca²⁺ cation, and H₂O molecule on both (001) and (010) surfaces. Copyright © 2016 John Wiley & Sons, Ltd.     

DFT studies on hydrogen‐bonding,Stacking, and XH···π‐Bonded systems in presence of external electric field

Effect of external electric field on interaction energy as well as stability of the hydrogen‐bonding, stacking, and O? H π‐bonded systems are analyzed in the light of density functional theory (DFT) and conceptual DFT. Interaction energy and stability measured in terms of global hardness and highest occupied molecular orbital energy of the considered systems are observed to be sensitive toward the strength and direction of the applied external electric field. The curvature of the potential energy surfaces gets changed in presence of an external electric field. © 2015 Wiley Periodicals, Inc.     

Substituent effects on 13C chemical shifts of ketenimines: a GIAO/HF and DFT study

GIAO/HF and DFT methods were utilized to predict the ¹³C chemical shifts of substituted ketenimines. GIAO HF/6–311+G(2d,p) and B3LYP/6–311+G(2d,p) methods were applied on the optimized B3LYP/6–31G(d) geometries and ¹³C chemical shifts of C_α and C_β of substituted ketenimines were correlated with group electronegativities. HF and DFT calculations indicated that increasing substituent group electronegativity leads to increasing chemical shift of C_β of substituted ketenimines, whereas the C_α values decrease. Copyright © 2003 John Wiley & Sons, Ltd.     

La3+’s Effect on the Surface (101) of Anatase for Methylene Blue Dye Removal,a DFT Study

Density functional theory (DFT) is a widely used method for studying matter at the quantum level. In this study, the surface (101) of TiO₂ (anatase phase) was considered to develop DFT calculations and explain the effect of lanthanum ion (La³⁺) on the electronic properties, adsorption capacity, and photocatalytic activity of this semiconductor. Due to the presence of the La³⁺ ion, the bandgap energy value of La/TiO₂ (2.98 eV) was lower than that obtained for TiO₂ (3.21 eV). TDOS analysis demonstrated the presence of hybrid levels in La/TiO₂ composed mainly of O2p and La5d orbitals. The chemical nature of the La-O bond was estimated from PDOS analysis, Bader charge analysis, and ELF function, resulting in a polar covalent type, due to the combination of covalent and ionic bonds. In general, the adsorption of the methylene blue (MB) molecule on the surface (101) of La/TiO₂ was energetically more favorable than on the surface (101) of TiO₂. The thermodynamic stability of doping TiO₂ with lanthanum was deduced from the negative heat-segmentation values obtained. The evidence from this theoretical study supports the experimental results reported in the literature and suggests that the semiconductor La/TiO₂ is a potential catalyst for applications that require sunlight.     

Effect of temperature on the EPR properties of a rhamnose alkoxy radical: a DFT molecular dynamics study

It has been shown previously that two distinctive variants (called RHop and RO4) exist of the radiation-induced rhamnose alkoxy radical. Density functional theory (DFT) calculations of the electron paramagnetic resonance (EPR) properties were found to be consistent with two separate measurements at different temperatures [E. Pauwels, R. Declerck, V. Van Speybroeck, M. Waroquier, Radiat. Res., in press]. However, the agreement between theory and experiment was only of a qualitative nature, especially for the latter radical. In the present work, it is examined whether this residual difference between theoretical and experimental spectroscopic properties can be explained by explicitly accounting for temperature in DFT calculations. With the aid of ab-initio molecular dynamics, a temperature simulation was conducted of the RO4 variant of the rhamnose alkoxy radical. At several points along the MD trajectory, g and hyperfine tensors were calculated, yielding time (and temperature) dependent mean spectroscopic properties. The effect of including temperature is evaluated but found to be within computational error.     

Efficient free energy calculations on small molecule host-guest systems - a combined linear interaction energy/one-step perturbation approach

Two efficient methods to calculate binding affinities of ligands with proteins have been critically evaluated by using sixteen small ligand host-guest complexes. It is shown that both the one-step (OS) perturbation method and the linear interaction energy (LIE) method have complementing strengths and weaknesses and can be optimally combined in a new manner. The OS method has a sound theoretical basis to address the free energy of cavity formation, whereas the LIE approach is more versatile and efficient to calculate the free energy of adding charges to such cavities. The off-term, which is neglected in the original LIE equation, can be calculated without additional costs from the OS, offering a powerful synergy between the two methods. The LIE/OS approach presented here combines the best of two worlds and for the model systems studied here, is more accurate than and as efficient as the original methods. It has a sound theoretical background and no longer requires any empirical parameters. The method appears very well suited for application in lead-optimization programmes in drug research, where the structure and dynamics of a series of molecules is of interest, together with an accurate calculation of the binding free energy.     

Activation and Conversion of Molecular Nitrogen to the Precursor of Ammonia on Silicon Substituted Cyclo[18]Carbon: a DFT Design

Recent synthesis of sp-hybridized cyclo[18]carbon allotrope has attracted immense curiosity. Since then, a generous amount of theoretical studies concerning aromaticity, adsorption, and spectra of the molecule have been performed. However, very few stuides have been carried out concerning its reactivities and catalytic behaviour. In this article, a DFT-based inquisition has been reported regarding the reactivity of Si substituted cyclo[18]carbon molecule towards molecular N₂. Results show that the Si substituted derivative is effective in producing adducts with molecular nitrogen. Charge calculations and IRC trapping methods indicate that only the Si center of C₁₇Si and its (HOMO-1) level participate in N₂ addition. The N-adduct so formed, is then found to spontaneously react with molecular H₂. The addition of two H₂ molecules to the activated nitrogen molecule to give respective amine derivatives have also been studied. The successful generation of the precursor of NH₃ by C₁₇Si lays a clear emphasis on its potentiality.     

Al-Decorated C2N Monolayer as a Potential Catalyst for NO Reduction with CO Molecules: A DFT Investigation

Developing efficient and economical catalysts for NO reduction is of great interest. Herein, the catalytic reduction of NO molecules on an Al-decorated C₂N monolayer (Al-C₂N) is systematically investigated using density functional theory (DFT) calculations. Our results reveal that the Al-C₂N catalyst is highly selective for NO, more so than CO, according to the values of the adsorption energy and charge transfer. The NO reduction reaction more preferably undergoes the (NO)₂ dimer reduction process instead of the NO direct decomposition process. For the (NO)₂ dimer reduction process, two NO molecules initially co-adsorb to form (NO)₂ dimers, followed by decomposition into N₂O and O_ads species. On this basis, five kinds of (NO)₂ dimer structures that initiate four reaction paths are explored on the Al-C₂N surface. Particularly, the cis-(NO)₂ dimer structures (D_cis-N and D_cis-O) are crucial intermediates for NO reduction, where the max energy barrier along the energetically most favorable pathway (path II) is as low as 3.6 kcal/mol. The remaining O_ads species on Al-C₂N are then easily reduced with CO molecules, being beneficial for a new catalytic cycle. These results, combined with its low-cost nature, render Al-C₂N a promising catalyst for NO reduction under mild conditions.     

Greener pastures in evaluating antidiabetic drug for a quinoxaline Derivative: Synthesis,Characterization, Molecular Docking,in vitro and HSA/DFT/XRD studies

In an effort to develop a potent antidiabetic drug, new quinoxaline derivative, 2-(4-((3-methyl-2-oxoquinoxalin-1(2H)-yl)methyl)-4,5-dihydro-1H-1,2,3-triazol-1-yl)-N-(p-tolyl)acetamide (MOQTA) was synthesized and characterized by XRD and various spectroscopic tools (IR, ¹H &¹³C NMR, ESI-MS). The geometric optimization of the molecule was calculated with Density Functional Theory (DFT) method by B3LYP with a 6–311++G(d,p) basis set. Frontier Molecular Orbitals (FMOs) and Molecular Electrostatic Potential (MEP) surfaces of the title compound were generated. Furthermore, Hirshfeld surface analysis (HSA) and 2D fingerprint plots were presented. The calculated MEP and HSA surface interactions were compared in terms of hydrogen bonds and π-π stacking interactions obtained by X-ray packing analyses. X-ray crystallographic structure analysis revealed that the N—HN, C—HO and C—HN intermolecular hydrogen bonds were in agreement with those obtained by HSA. Moreover, MOQTA was assessed for its in vitro anti-diabetic activity. Likewise, molecular docking analyses were conducted to examine the binding mode between MOQTA and the enzymes α-glucosidase and α-amylase. Finally, the physicochemical, pharmacokinetic and toxicological properties of MOQTA have been evaluated by using in silico absorption, distribution, metabolism, excretion and toxicity analysis prediction.