Computational Study of the Sulfonylated Amino Acid Hydroxamates Binding to the Zinc Ion within the Active Site of Carbonic Anhydrase

Abstract

The B3LYP/6–311+G(d,p) method and three ONIOM extrapolation methods ONI-OM (B3LYP/6–311+G(d,p): AM1); ONIOM(B3LYP/6–311+G(d,p): MNDO); ONIOM (B3LYP/6–311+G(d,p): HF/3-21G(d)) were used to characterize the complexes of Zn²⁺ cation with anionic sulfonylated amino acid hydroxamates (RSO₂NH-AA-CON(-)OH), possessing an unsubstituted RSO₂NH—amino acyl moiety. According to the R moiety we distinguish between pentafluorophenyl and 4-methoxyphenyl derivates. The amino acid hydroxamates included in the study were the Gly, Ala, and Leu derivates. Of the inhibitors investigated, the weakest zinc affinity exhibits the pentafluorophenyl derivate with Gly amino acid and the strongest affinity the 4-methoxyphenyl derivate with Leu amino acid. The inhibitors form bidentate coordination bonds with the zinc cation by means of the sulfonyl oxygen and the ionized hydroxamate nitrogen atoms, respectively. The zinc affinities computed using the B3LYP/6–311 +G(d,p)//HF/6–31 +G(d,p) method are in very good agreement with the full density functional theory (DFT) B3LYP/6–311+G(d,p)//B3LYP/6- 311+G(d,p) method and this method can be adopted to model larger complexes of inhibitors with the active site of carbonic anhydrase.     

Theoretical study of the pre- and post-translational effects of adenine and thymine tautomers and methyl derivatives

The study of pre-translational effects (ionization, tautomerization) and post-translational effects (methylation) of adenine and thymine has only recently been the focus of some studies. These effects can potentially help regulate gene expression as well as potentially disrupt normal gene function. Because of this wide array of roles, greater insight into these effects in deoxyribonucleic acids (DNA) are paramount. There has been considerable research of each phenomenon (tautomerization, methylation and ionization) individually. In this work, we attempt to shed light upon the pre-translational effects and post translational effects of adenine and thymine by investigating the electron affinities (EAs) and ionization potentials (IPs) of the major and minor tautomers and their methyl derivatives. We performed all calculations using the density functional theory (DFT) B3LYP functional accompanied with 6-311G(d,p), 6-311+G(d,p) and 6-311++G(df,pd) basis sets. Our results reveal that the thymine tautomer has a higher EA and IP than the adenine tautomers. The higher EA suggests that an electron that attaches to the AT base pair would predominately attach to the thymine instead of adenine. The higher IP would suggest that an electron that is removed from the AT base pair would be predominately removed from the adenine within the base pair. Understanding how tautomerization, ionization and methylation differences change effects, discourages, or promotes one another is lacking. In this work, we begin the steps of integrating these effects with one another, to gain a greater understanding of molecular changes in DNA bases.     

Studies on structures and electron affinities of the simplest alkyl dithio radicals and their anions with gaussian-3 theory and density functional theory

The equilibrium geometries and electron affinities of the R-SS/R-SS^-(R=CH₃, C₂H₅, n-C₃H₇, i-C₃H₇, n-C₄H₉, t-C₄H₉, n-C₅H₁₁) species have been studied using the higher level of the Gaussian-3(G3) theory and 21 carefully calibrated pure and hybrid density functionals (five generalized gradient approximation (GGA) methods, seven hybrid GGAs, three meta GGA methods, and six hybrid meta GGAs) in conjunction with diffuse function augmented double-ζ plus polarization (DZP++) basis sets. The geometries are fully optimized with each method and discussed. The reliable adiabatic electron affinity has been presented by means of the high level of G3 technique. With the DZP++ DFT method, three measures of neutral/anion energy differences reported in this work are the adiabatic electron affinity, the vertical electron affinity, and the vertical detachment energy. The adiabatic electron affinities, obtained at the BP86, M05-2X, B3LYP, M06, B98, M06-2X, mPW1PW91, HCTH, B97-1, M05, PBE1PBE, and VSXC methods, are in agreement with the G3 results. These methods perform better for EA prediction and are considered to be reliable.     

Quantum-chemical investigation of the structure and the antioxidant properties of α-lipoic acid and its metabolites

Quantum-chemical computations were used to investigate the structure-antioxidant parameter relationships of α-lipoic acid and its natural metabolites bisnorlipoic acid and tetranorlipoic acid in their oxidized and reduced forms. The enantiomers of lipoic and dihydrolipoic acid were optimized using the B3LYP/6-311+G(3df,2p), B3LYP/aug-cc-pVDZ and MP2(full)/6-31+G(d,p) levels of theory as isolated molecules and in the presence of water. The geometries of the metabolites and the values of their antioxidant parameters (proton affinity, bond dissociation enthalpy, adiabatic ionization potential, spin density, and the highest occupied molecular orbital energy) were calculated at the B3LYP/6-311+G(3df,2p) level of theory. The results obtained reveal similarities between these structures: a pentatomic, nonaromatic ring is present in the oxidized forms, while an unbranched aliphatic chain (as found in saturated fatty acids) is present in both the oxidized and the reduced forms. Analysis of the spin density and the highest occupied molecular orbital energy revealed that the SH groups exhibited the greatest electron-donating activities. The values obtained for the proton affinity, bond dissociation enthalpy and adiabatic ionization potential indicate that the preferred antioxidant mechanisms for α-lipoic acid and its metabolites are sequential proton loss electron transfer in polar media and hydrogen atom transfer in vacuum.     

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.     

Comparative theoretical study of the UV/Vis absorption spectra of styrylpyridine compounds using TD-DFT calculations

This study examined absorption properties of 2-styrylpyridine, trans-2-(m-cyanostyryl)pyridine, trans-2-[3-methyl-(m-cyanostyryl)]pyridine, and trans-4-(m-cyanostyryl)pyridine compounds based on theoretical UV/Vis spectra, with comparisons between time-dependent density functional theory (TD-DFT) using B3LYP, PBE0, and LC-ωPBE functionals. Basis sets 6–31G(d), 6–31G(d,p), 6–31+G(d,p), and 6–311+G(d,p) were tested to compare molecular orbital energy values, gap energies, and maxima absorption wavelengths. UV/Vis spectra were calculated from fully optimized geometry in B3LYP/6–311+G(d,p) in gas phase and using the IEFPCM model. B3LYP/6–311+G(d,p) provided the most stable form, a planar structure with parameters close to 2-styrylpyridine X-ray data. Isomeric structures were evaluated by full geometry optimization using the same theory level. Similar energetic values were found: ～4.5 kJ?mol^?1 for 2-styrylpyridine and ～1 kJ?mol^?1 for derivative compound isomers. The 2-styrylpyridine isomeric structure differed at the pyridine group N-atom position; structures considered for the other compounds had the cyano group attached to the phenyl ring m-position equivalent. The energy difference was almost negligible between m-cyano-substituted molecules, but high energy barriers existed for cyano-substituted phenyl ring torsion. TD-DFT appeared to be robust and accurate approach. The B3LYP functional with the 6–31G(d) basis set produced the most reliable λ_max values, with mean errors of 0.5 and 12 nm respect to experimental values, in gas and solution, respectively. The present data describes effects on the λ_max changes in the UV/Vis absorption spectra of the electron acceptor cyano substituent on the phenyl ring, the electron donor methyl substituent, and the N-atom position on the electron acceptor pyridine ring, causing slight changes respect to the 2-styrylpyridine title compound.     

Absolute configuration of (−)-myrtenal by vibrational circular dichroism

The VCD spectrum of the monoterpene (−)-myrtenal (1) was compared with theoretical spectra using ab initio density functional theory (DFT) calculations at the B3LYP/6-31G(d,p), B3LYP/6-31G+(d,p), B3LYP/6-311G+(d,p), B3LYP/DGDZVP, and B3PW91/DGTZVP levels of theory. Conformational analysis of 1 indicated that the lowest energy conformer was s-trans-C2-C10, which contributes more than 98.5% to the total conformational population regardless of the employed level of theory. The use of a recently developed confidence level algorithm demonstrated that VCD spectra calculated for the main conformer, using the indicated hybrid functionals and basis set, gave no significant changes, from where it follows that B3LYP/DGDZVP calculations provide a superior balance between computer cost and VCD spectral accuracy. The DGDZVP basis set demanded around a quarter the time than the 6-311G+(d,p) basis set while providing similar results. The spectral comparison also provided evidence that the levorotatory enantiomer of myrtenal has the 1R absolute configuration.     

Probing the antioxidant potential of phloretin and phlorizin through a computational investigation

The structures and energetics of two dihydrochalcones (phloretin and its glycoside phlorizin) were examined with density functional theory, using the B3LYP, M06-2X, and LC-ω PBE functionals with both the 6-311G(d,p) and 6-311 + G(d,p) basis sets. Properties connected to antioxidant activity, i.e., bond dissociation enthalpies (BDEs) for OH groups and ionization potentials (IPs), were computed in a variety of environments including the gas-phase, n-hexane, ethanol, methanol, and water. The smallest BDEs among the four OH groups for phloretin (three for phlorizin) were determined (using B3LYP/6-311 + G(d,p) in water) to be 79.36 kcal/mol for phloretin and 79.98 kcal/mol for phlorizin while the IPs (at the same level of theory) were obtained as 139.48 and 138.98 kcal/mol, respectively. By comparing with known antioxidants, these values for the BDEs indicate both phloretin and phlorizin show promise for antioxidant activity. In addition, the presence of the sugar moiety has a moderate (0-6 kcal/mol depending on functional) effect on the BDEs for all OH groups. Interestingly, the BDEs suggest that (depending on the functional chosen) the sugar moiety can lead to an increase, decrease, or no change in the antioxidant activity. Therefore, further experimental tests are encouraged to understand the substituent effect on the BDEs for phloretin and to help determine the most appropriate functional to probe BDEs for dihydrochalcones.     

Density functional theory study of N-H...O, O-H...O and C-H...O hydrogen-bonding effects on the 14N and 2H nuclear quadrupole coupling tensors of N-acetyl-valine

Hydrogen-bonding effects in the crystalline structure of N-acetyl-valine, NAV, were studied using the (14)N and (2)H quadrupole coupling tensors via density functional theory. The calculations were carried out at the B3LYP level with the 6-311++G(d,p) and 6-311+G(d) basis sets. The theoretical quadrupole coupling components and their relative orientation in the molecular frame axes at the nitrogen site are compared to experimental values. This nucleus is involved in a rather strong intermolecular O=CNH...O=CNH hydrogen bond, r(N-H...O(1))=2.04 A and angleN-H...O(1)=171.53 degrees. A reasonably good agreement between the experimentally obtained (2)H quadrupole coupling tensors and the B3LYP/6-311++G(d,p) calculations is achievable only in molecular model where a complete hydrogen-bonding network is considered.     

Gas-phase metal ion (Li+, Na+, Cu+) affinities of glycine and alanine

The gas-phase metal affinities of glycine and alanine for Li+, Na+ and Cu+ ions have been determined theoretically employing the hybrid B3LYP exchange-correlation functional and using extended basis sets. All computations indicate that the metal ion affinity (MIA) decreases on going from Cu+ to Li+ and Na+ for both the considered amino acids. The absolute MIA values are close to the experimental counterparts with the exception of lithium for which a deviation of about 7 kcal/mol at the B3LYP level is obtained. The optimized structures indicate that Li+, Na+ and Cu+ prefer a bidentate coordination, bonding with both nitrogen and oxygen atoms of amino acids.     

Molecular structure,vibrational spectroscopic,NBO and HOMO–LUMO studies of 2-amino 6-bromo 3-formylchromone

A systematic quantum mechanical study of the possible conformations and vibrational spectra of 2-amino 6-bromo 3-formylchromone has been reported. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by Hartree–Fock and density functional theory employing Becke's three-parameter (local, non-local and HF) hybrid exchange functionals with Lee–Yang–Parr co-relational (B3LYP) functionals using 6-311++G(d,p) basis set with complete relaxation in the potential energy surface. The calculated wavenumbers after proper scaling show a very good agreement with the observed values. The electrostatic potential mapped onto isodensity surface has been obtained. The natural bond orbital analysis has been carried out in order to study the intra-molecular bonding, interactions among bonds and delocalisation of unpaired electrons. The highest occupied molecular orbital–lowest unoccupied molecular orbital studies have been conducted in order to determine the way the molecule interacts with other species.     

H-bonded complexes between acetylacetone and two molecules of methanol: HF and DFT level study

Five stable H-bonded complexes (supersystems) between acetylacetone and two methanol molecules were investigated at the B3LYP and HF levels of theory using the 6-311G** and 6-11++G** basis sets. The most stable complex was found as the one with the highest relative bonding and interaction energies. All vibrational frequencies resulting from calculations with the 6-311++G** basis set were compared with the recorded IR spectrum of acetylacetone/methanol mixture in a molar ratio 1:2.     

Extrapolation of water and formaldehyde harmonic and anharmonic frequencies to the B3LYP/CBS limit using polarization consistent basis sets

The harmonic and anharmonic frequencies of fundamental vibrations in formaldehyde and water were successfully estimated using the B3LYP Kohn-Sham limit. The results obtained with polarization- and correlation-consistent basis sets were fitted with a two-parameter formula. Anharmonic corrections were obtained by a second order perturbation treatment (PT2). We compared the performance of the PT2 scheme on the two title molecules using SCF, MP2 and DFT (BLYP, B3LYP, PBE and B3PW91 functionals) methods combined with polarization consistent pc-n (n = 0, 1, 2, 3, 4) basis sets, Dunning’s basis sets (aug)-cc-pVXZ where X = D, T, Q, 5, 6 and Pople’s basis sets up to 6-311++G(3df,2pd). The influence of SCF convergence level and density grid size on the root mean square of harmonic and anharmonic frequency deviations from experimental values was tested. The wavenumber of formaldehyde CH₂ anharmonic asymmetric stretching mode is very sensitive to grid size for large basis sets; this effect is not observed for harmonic modes. BLYP-calculated anharmonic frequencies consistently underestimate observed wavenumbers. On the basis of formaldehyde anharmonic frequencies, we show that increasing the Pople basis set size does not always lead to improved agreement between anharmonic frequencies and experimental values.     

Molecular structure,vibrational spectra and HOMO,LUMO analysis of 4-piperidone by density functional theory and ab initio Hartree–Fock calculations

Vibrational frequencies and geometrical parameters of 4-piperidone (4-PID) in the ground state have been calculated by using the Hartree–Fock (HF) and density functional methods (B3LYP) with 6-311++G(d,p) and 6-311+G(3df,2p) basis sets. These methods are proposed as a tool to be applied in the structural characterisation of 4-PID (C₅H₉NO). The title molecule has C _s point group symmetry, thus providing useful support in the interpretation of experimental IR and Raman data. The DFT-B3LYP/6-311+G(3df,2p) calculations have been found more reliable than the ab initio HF/6-311++G(d,p) calculations for the vibrational study of 4-PID. The calculated highest occupied molecular orbital and lowest unoccupied molecular orbital energies show that charge transfer occurs within the molecule. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title molecule have been constructed.     

Studies on molecular structure and tautomerism of a vitamin B<Subscript>6</Subscript> analog with density functional theory

This work presents a computational study on the molecular structure and tautomeric equilibria of a novel Schiff base L derived from pyridoxal (PL) and o-phenylenediamine by using the density functional method B3LYP with basis sets 6-31 G(d,p), 6-31++G(d,p), 6-311 G(d,p) and 6-311++G(d,p). The optimized geometrical parameters obtained by B3LYP/6-31 G(d,p) method showed the best agreement with the experimental values. Tautomeric stability study of L inferred that the enolimine form is more stable than its ketoenamine form in both gas phase and solution. However, protonation of the pyridoxal nitrogen atom (LH) have accelerated the formation of ketoenamine form, and therefore, both ketoenamine and enolimine forms could be present in acidic media.     

Spin states of Mn(III) meso-tetraphenylporphyrin chloride assessed by density functional methods

The present work assessed several exchange-correlation functionals (including GGA, meta-GGA and hybrid functionals), in combination with a variety of basis sets and effective core potentials (ECP) for their ability to predict the ground spin state of Mn(III) meso-tetraphenylporphyrin chloride complex, labeled Mn(III)TPPCl, for which experimental data support the quintet high spin state. Geometry optimization of Mn(III)TPPCl was performed for three possible spin states (singlet state, LS; triplet state, IS; and quintet state, HS) at the TPSSh level using the LANL2DZ ECP for Mn and the 6-311G(d) basis set for C, N, Cl and H. Afterwards, single-point energy calculations were conducted by applying 18 exchange-correlation functionals (BLYP, B3LYP, PW91, BPW91, BP86, OLYP, OPBE, OPW91, O3LYP, PBE0, PBEh1PBE, HSEH1PBE, TPSS, TPSSh, M06 L, M06, M062X and M06HF). The influence of the basis set for the metal center was assessed using a smaller group of functionals and varying between the Pople basis set 6-31G(d), its newer formulation m6-31G(d) and the larger Def2-QZVP basis set. All functionals in combination with Pople basis sets predict the quintet state as the ground spin state. In addition, the BLYP, BP86, BPW91, PW91, PBEh1PBE, TPSS and TPSSh functionals predicted the IS lying at most ~60 kJ mol^?1 above the HS, which agrees with the reference data. Results including Def2-QZVP basis set were inconsistent, since only BLYP and B3LYP predict HS as the ground spin state. The recommended methodology for the treatment of such systems seems to be exchange-correlations functionals with few or none Hartree-Fock exchange and modest size basis sets.

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Graphical Abstract MnTPPCl molecule and the energy ordering of its spin states assessed by 18 functionals

     

A computational investigation on the antioxidant potential of myricetin 3,4′-di-<Emphasis Type="Italic">O</Emphasis>-<Emphasis Type="Italic">α</Emphasis>-<Emphasis Type="Italic">L</Emphasis>-rhamnopyranoside

In this work, we present a computational study on the antioxidant potential of myricetin 3,4\(^{\prime }\)-di-O-α-L-rhamnopyranoside (Compound M). A density functional theory (DFT) approach with the B3LYP and LC-ωPBE functionals and with both the 6-311G(d,p) and 6-311+G(d,p) basis sets was used. The focus of the investigation was on the structural and energetic parameters including both bond dissociation enthalpies (BDEs) and ionization potentials (IPs), which provide information on the potential antioxidant activity. The properties computed were compared with BDEs and IPs available in the literature for myricetin, a compound well known for presenting antioxidant activity (and the parent molecule of the compound of interest in the present work). Myricetin 3,4\(^{\prime }\)-di-O-α-L-rhamnopyranoside presented the lowest BDE to be 79.13 kcal/mol (as determined using B3LYP/6-311G(d,p) in water) while myricetin has a quite similar value (within 3.4 kcal/mol). IPs computed in the gas phase [B3LYP/6-311G(d,p)] are 157.18 and 161.4 kcal/mol for myricetin 3,4\(^{\prime }\)-di-O-α-L-rhamnopyranoside and myricetin, respectively. As the values of BDEs are considerably lower than the ones probed for IPs (in the gas phase or in any given solvent environment), the hydrogen atom transfer mechanism is preferred over the single electron transfer mechanism. The BDEs obtained suggest that myricetin 3,4\(^{\prime }\)-di-O-α-L-rhamnopyranoside can present antioxidant potential as good as the parent molecule myricetin (a well-known antioxidant). Therefore, experimental tests on the antioxidant activity of Compound M are encouraged.     

Performance of density functionals for the structure and energetics of (M–O)0,± (M=Al,Si, Sc–Zn)

We report the results of the performance of 20 exchange–correlation functionals of density functional theory (DFT) in the structure (Metal–Oxygen bond length) and energetical properties (bond dissociation energy, adiabatic ionisation energy, and adiabatic electron affinity) of twelve metal monoxides (M–O, M=Al, Si, Sc–Zn). The calculated results show that the selected DFT functionals have the ability to reproduce the M–O bond length with a mean deviation of 0.01–0.05 Å, the energy values are reproduced with a mean deviation of 0.20–1.00?eV. In general, the functionals with significant HF exchange show decent performance in the calculation of bond length and harmonic vibrational frequency. These functionals show poor performance in energetics. Our calculated results show that the M06-L, B3LYP, and TPSSh functionals give good performance in both structure and energetical properties of metal monoxides. These functionals are recommended for the studies of structure and energetics in metal oxide systems. Further, our studies indicate that M06-L can be used for the studies in larger molecular systems. Among the 20 DFT functionals, the recently developed N12 functional gives poor performance in the studies of metal monoxides. Hence this functional is not recommended for the studies of structure and energetics in metal oxide systems.     

Comparison of gas phase intrinsic properties of cytosine and thymine nucleobases with their O-alkyl adducts: different hydrogen bonding preferences for thymine versus O-alkyl thymine

In recent years, there has been increasing interest in damaged DNA and RNA nucleobases. These damaged nucleobases can cause DNA mutation, resulting in various diseases such as cancer. Alkylating agents are mutagenic and carcinogenic in a variety of prokaryotic and eukaryotic organisms. The present study employs density functional theory (DFT/B3LYP) with the 6-311++G(d,p) basis set to investigate the effect of chemical damage in O-alkyl pyrimidines such as O⁴-methylthymine, O²-methylcytosine and O²-methylthymine. We compared the intrinsic properties, such as proton affinities, gas phase acidities, equilibrium tautomerization and nucleobase pair’s hydrogen bonding properties, of these molecules with those in the normal nucleobases thymine and cytosine. The results are of interest for chemical reasons and also possibly for biological purposes since biological media can be quite non-polar. Furthermore, we found that N1-H of O⁴-methylthymine is less acidic than N1-H of thymine, suggesting that alkyl DNA glycosylase enzyme cannot discriminate this damaged nucleobase from a normal thymine nucleobase. This result indicates that the conjugated base anion of O⁴-methylthymine would be a worse leaving group and O⁴-methylthymine is repaired in genome by demethylation rather than enzyme-catalyzed excision at N1.