DFT investigation on the structural and vibrational behaviours of the non-protein amino acids in hybrid explicit/continuum solvent: a case of the zwitterions γ-aminobutyric and α - aminoisobutyric acids

BACKGROUND

The influence of hybrid solvation models on the molecular structures and vibrational characteristics of g-aminobutyric acid (GABA) and a-aminoisobutyric acid (AIB) zwitterions was assessed by employing a variety of Density Functional Theory (DFT). The quantum chemical methods included the B3LYP and B3PW91 hybrid functionals and the 6‑311++G(d,p) basis set.

METHODS

The most stable conformation derived from the potential energy surface (PES) scans using the B3LYP/6-311++G(d,p) model chemistry for each studied molecule was predicted within a continuum environment represented by the COSMO and SMD solvation models. The stable structures were subsequently immersed in explicit/COSMO and explicit/SMD hybrid solvation models, where 10 and 8 water molecules were explicitly positioned around the functional groups of the GABA and AIB zwitterions, respectively. The number of water molecules chosen was sufficient to prevent proton transfer among the carboxylate group (COO-) and the ammonium group (NH3+) within each molecule under investigation. After optimizing the geometry of each hydrated complex, the normal vibrational modes were determined. The scaled theoretical frequencies obtained from the various model chemistries were then compared to available experimental data from infrared (IR) and Raman spectroscopy.

RESULTS

In the case of GABA and AIB molecules, the comparisons revealed that the B3LYP/6-311++G(d,p) model chemistry yielded wavenumber values that closely matched the experimental IR and Raman data, particularly when the explicit/SMD solvent was employed. The computed results indicate deviations of less than 4% when compared to the experimental data for the two molecules under investigation.

Spectroscopic, quantum chemical, molecular docking and molecular dynamics investigations of hydroxylic indole-3-pyruvic acid: a potent candidate for nonlinear optical applications and Alzheimer's drug

In this paper, a complete theoretical investigation of hydroxylic indole-3-pyruvic acid (HIPyA) molecule was performed using the DFT quantum chemical, molecular docking and molecular dynamics calculations. The conformational analysis of HIPyA molecule was carried out using density functional theory quantum chemical calculations. The most stable structure of the studied molecule was predicted by means of DFT/B3LYP method with cc-pVTZ basis set. The simulated vibrational frequencies were assigned and proved to be in agreement with the available experimental FT-IR data. The effects of gas phase and solvents on UV-visible spectra of HIPyA molecule were simulated using TD-DFT/B3LYP method with cc-pVTZ basis set. The analysis of the density of states spectrum validates the frontier molecular orbitals results, which reveals the charge transfer interaction in HIPyA molecule. The molecular electrostatic potential surface confirms the electrophilic and nucleophilic reactive sites of the studied molecule. The natural bond orbital analysis evidences the bioactivity of the studied molecule. The obtained first order hyperpolarizability value is 33.596 times greater than urea, which confirms the nonlinear optical activity of HIPyA molecule. The molecular docking analysis reveals that the studied molecule under interest can act as a potent inhibitor against the amyloid β-protein (Aβ) enzyme, which causes the Alzheimer's disease. The molecular dynamics analysis confirms the reliability of the docking results.Communicated by Ramaswamy H. Sarma.

Reaction of •OH with CHCl=CH-CHF2 and its atmospheric implication for future environmental-friendly refrigerant

In order to understand the atmospheric implication of the chlorinated hydrofluoroolefin (HFO), the geometrical structures and the IR absorption cross sections of the stereoisomers 1-chloro-3,3-difluoropropene were studied using the B3LYP/6-31G(3df) and M06-2X/6-31G(3df) methods in the gas phase. The cis-trans isomerization was assessed using the M06-2X/6-311++G(3df,p)//6-31+G(3df,p) method. The latter method was also employed for thermochemistry and the rate coefficients of the reactions of •OH with the cis- and trans-isomers in the temperature ranging from 200 to 400 K. The computational method CCSD/cc-pVTZ//M06-2X/6-31+G(3df,p) was used to benchmark the rate coefficients. It turns out that, the trans-isomer is more stable than cis-isomer and the trans- to cis-isomerization is thermodynamically unfavorable. The rate coefficient follows the Gaussian law with respect to the inverse of temperature. At the global temperature of stratosphere, the calculated rate coefficients served to estimate the atmospheric lifetime along with the photochemical ozone creation potential (POCP). This yielded lifetimes of 4.31 and 7.31 days and POCPs of 3.80 and 2.23 for the cis- and trans-isomer, respectively. The radiative forcing efficiencies gave 0.0082 and 0.0152 W m−2 ppb−1 for the cis- and trans-isomer, respectively. The global warming potential approached zero for both stereoisomers at 20, 100, and 500 years time horizons.

Characterization of engine lubricants by fluorescence spectroscopy and chemometrics

In this study, principal component analysis (PCA) and parallel factor analysis (PARAFAC) combined with excitation-emission matrix fluorescence (EEMF) were used to determine the most efficient excitation wavelengths of engine lubricants; identify their fluorophores; classify them and look for correlations between their fluorescence and their physical parameters. EEMF spectra were obtained for the different samples in the range of 260 to 600 nm, and 300 to 700 nm for excitation and emission wavelengths respectively. PCA and PARAFAC showed that the efficient excitation wavelengths for engine lubricants are 300, 350, 400, 450 and 470 nm. These five wavelengths represented the maxima of the PARAFAC recovered excitation profiles, of which two were attributed to fluorene and pyrene. The relative proportions of the PARAFAC retrieved components were used to classify engine lubricants with a satisfactory percentage of classification of 70%. Finally, a good correlation was obtained between some physical parameters (particularly the viscosity) of engine lubricants and their fluorescence.

Structures and relative stability of hydrated ferrous ion clusters and temperature effects

Structures of solvated ferrous ion clusters have been investigated in the singlet and quintet spin states of the ferrous ion. Relative stabilities of isomers are also discussed at different temperatures.

Insight of UV-vis spectra and atmospheric implication for the reaction of ˙OH radical towards glyphosate herbicide and its hydrates

The rate constant of the reactions of ˙OH radicals with glyphosate (GPS) and its hydrates (GPS(H₂O)_n=1–3) were evaluated using the dual method M06-2X/6-311++G(df,p)//6-31+G(df,p) over the temperature range of 200–400 K. The results served to estimate the atmospheric lifetime along with the photochemical ozone creation potential (POCP). The calculations yielded an atmospheric lifetime of 2.34 hours and a POCP of 24.7 for GPS. Upon addition of water molecules, there is an increase of lifetime and decrease of POCP for water monomer and water dimer. The POCP for water trimer is slightly above the gaseous GPS. However, the POCPs of GPS and its hydrates are comparable to that of alkanes. The GPS and its hydrates were found to be a potential reservoir of CO₂. The acidification potential (AP) of GPS was found to be 0.189 and decreases upon addition of water molecules. This shows negligible contribution to rain acidification as the AP is less than that of SO₂. The UV-vis spectra were attained using the M06-L/6-311++G(3df,3pd) method and cover the range 160–260 nm which fits well with experiment.

The rate constant of the reactions of ˙OH radical with glyphosate (GPS) and its hydrates (GPS(H₂O)_n=1–3) were evaluated using the dual method M06-2X/6-311++G(df,p)//6-31+G(df,p) over the temperature range of 200–400 K.

Effects of counterions and solvents on the geometrical and vibrational features of dinucleoside-monophosphate (dNMP): case of 3',5'-dideoxycytidine-monophosphate (dDCMP)

The effects of the interaction of the monovalent (Li⁺, Na⁺, K⁺) and divalent (Mg²⁺) counterions hexahydrated (6H₂O), with the PO₂^- group, on the geometrical and vibrational characteristics of 3', 5'-dDCMP, were studied using the DFT/B3LYP/6-31++G(d) method. These calculations were performed using the explicit (6H₂O) and hybrid (6H₂O/Continuum) solvation models. The optimizations reveal that in the conformation g^-g^- and in the explicit model of solvation, the small ions (Li⁺, Na⁺) deviate from the bisector plane of the angle O1-P-O2 and the large ions (K⁺ and Mg²⁺) remain in this plane, whereas in the hybrid model of solvation, the counterions deviate from this plane. However, when the conformer is g⁺g⁺, the monovalent counterions deviate and divide the remainder of the plane regardless of the type of solvation model. In addition, the g^-g^- conformer is the most stable in the presence of the explicit solvent, while the g⁺g⁺ conformer is the most stable in the presence of the hybrid solvent. Finally, the normal modes of the conformers g^-g^- and g⁺g⁺ in the presence of the counterions in the hybrid model show a better agreement with the available experimental data of the DNA forms A, B (g^-g^-), and Z (g⁺g⁺) relatively to the explicit model. This very good agreement is illustrated by the very small deviations ≤ 0.08% (g^-g^-) and ≤ 0.41% (g⁺g⁺) observed between the calculated and experimental data for the PO₂^- (asymmetric) stretching mode in the presence of the counterion K⁺ in the hybrid model. Graphical abstract.

Structures of the solvated copper(ii) ion in ammonia at various temperatures

We investigated theoretically the structures and relative stabilities of the solvated copper(ii) ion in ammonia, Cu²⁺(NH₃)_n, n = 1–10.

Electronic transitions and ESIPT kinetics of the thienyl-3-hydroxychromone nucleobase surrogate in DNA duplexes: a DFT/MD-TDDFT study

The fluorescent nucleobase surrogate M (2-thienyl-3-hydroxychromone fluorophore) when imbedded in DNA opposite an abasic site exhibits a two colour response highly sensitive to environment changes and base composition. Its two colour emission originates from an excited state intramolecular proton transfer (ESIPT), which converts the excited normal N* form into its T* tautomer. To get deeper insight on the spectroscopic properties of M in DNA duplexes, quantum chemical calculations were performed on M stacked with different base pairs in model trimers extracted from MD simulations. The photophysics of M in duplexes appeared to be governed by stacking interactions as well as charge and hole transfer. Indeed, stacking of M in DNA screens M from H-bonding with water molecules, which favours ESIPT and thus, the emission of the T* form. With A and T flanking bases, the electronic densities in the frontier MOs were localized on M, in line with its effective absorption and emission. In addition, reduction of the free rotation between the thienyl and chromone groups together with the shielding of the dye from water molecules largely explain its enhanced quantum yield in comparison to the free M in solution. By contrast, the localisation of the electron density on the flanking G residues in the ground state and the energetically favorable hole transfer from M to G in the excited state explains the reduced quantum yield of M sandwiched between CG pairs. Finally, the much higher brightness of M as compared to 2-aminopurine when flanked by A and T residues could be related to the much stronger oscillator strength of its S₀ → S₁ transition and the ineffective charge transfer from M to A or T residues.

The fluorescent nucleobase surrogate M (2-thienyl-3-hydroxychromone fluorophore) when imbedded in DNA opposite an abasic site exhibits a two colour response highly sensitive to environment changes and base composition.

DFT Study of Photochemical Properties and Radiative Forcing Efficiency Features of the Stereoisomers cis- and trans-CHCl═CH-CF3

The accurate assessment of radiative forcing efficiency (RFE) of a greenhouse gas is based on the precise knowledge of its structure and infrared absorption spectrum. The present work investigates the UV-vis absorption spectra and IR absorption spectra that are used for the determination of RFE of the short-lived compounds, cis- and trans-CHCl═CHCF₃ (CTFP). These investigations were carried out with six different density functional theory (DFT) methods B3LYP, CAM-B3LYP, M06, M06-2X, TPSS0, and ωB97X-D associated to the basis set 6-31G(3df). Therefrom, the relative populations of the two states cis and trans for temperatures over the range 220-370 K at 1 atm and along the atmospheric altitude were assessed. It turns out that trans-CTFP is the abundant component between the two states. This review reveals that B3LYP and M06 reproduce well the experimental results of UV-vis spectra of trans-CTFP. As for cis-CTFP, EOM-CCSD is not well fitted by DFT methods. The cis- to trans-CTFP isomerization leads to the red shift for DFT methods and to the blue shift in regard to EOM-CCSD and experimental results. The IR absorption spectra are well fitted by B3LYP over the range 500-1600 cm^-1 and TPSS0 over 1300-2000 cm^-1 for both stereoisomers. Moreover, the root-mean-square errors (RMSEs) of frequencies from experimental data are lower for B3LYP and TPSS0 for both systems. The computed IR absorption band strengths over 500-2000 cm^-1 for cis- and over 600-1800 cm^-1 for trans-CTFP are consistent with the experiment. The relevant descriptor RFEs of the climate effect were calculated using a narrow band model for a constant vertical profile and then corrected with a lifetime factor for different computational methods. The computed values correlate well with the experimental results for both stereoisomers except M06-2X and TPSS0. It is worth noting that, for both systems, the intense radiative forcing spectra are located at frequencies ranging in 1000-1200 cm^-1. The lower forcings of trans-CTFP lying in the atmospheric window region 800-1000 cm^-1 are greater than those of cis-CTFP. Therefore, RFE(trans-CTFP) = 1.127 RFE(cis-CTFP).

Thermodynamic of solvation, solute - Solvent electron transfer and ionization potential of BSCAPE molecule and its UV-vis spectra in aqueous solution

The molecular system 2-Phenylethyl (2E)-3-(1-benzenesulfonyl-4,5-dihydroxyphenyl) acrylate (BSCAPE) is a phenolic acid that covers a large spectrum of biological properties. The investigations of solvation and oxidation processes of BSCAPE molecule by computational means were the challenge of this present work. Water was required for solvation throughout the work. The explicit H₂O were sequentially added to form the complexes BSCAPE(H₂O)_n=0-11. The discrete - continuum model was at the heart of this work. DFT and TD-DFT both associated to the continuum model SMD were required. Hence, the structures, the solvation energies, the energies of solute - solvent electron transfer (SSET), the ionisation potential (IP), and the UV-vis spectra were studied. It comes out that, the structure of the CAPE part included in BSCAPE agrees well with the available experimental values of CAPE but with a minor influence due to the presence of benzensulfonyl group. The enthalpy and free energy of solvation increase linearly with nH₂O. The global reactivity indexes were assessed to appreciate the oxidation of BSCAPE. The latter quality was strongly assessed by the enthalpy and free energy of SSET and IP. The SSET potential increase with nH₂O and the size of water clusters. The values 723.16 and 711.62 kJ/mol were found for enthalpy and free energy of IP respectively. Then in aqueous solution, the results fall down and upon addition of nH₂O, they approach gas phase value for 11H₂O and still are not stabilized. Therefore, the resistance to oxidation starts to raise at this level. Elsewhere, the UV-vis spectra of BSCAPE present four important peaks about 279.3, 234.8, 208.4 and 199.4 nm in gaseous state. The excitation shifts to the red as the number of H₂O increase. Their oscillator strengths also increase with solvation.

DFT study of geometrical and vibrational features of a 3',5'-deoxydisugar-monophosphate (dDSMP) DNA model in the presence of counterions and solvent

The B3LYP/6-31++G* theoretical level was used to study the influence of various hexahydrated monovalent (Li⁺, Na⁺, K⁺) and divalent (Mg²⁺) metal counterions in interaction with the charged PO₂^- group, on the geometrical and vibrational characteristics of the DNA fragments of 3',5'-dDSMP, represented by four conformers (g⁺g⁺, g⁺t, g^-g^- and g^-t). All complexes were optimized through two solvation models [the explicit model (6H₂O) and the hybrid model (6H₂O/Continuum)]. The results obtained established that, in the hybrid model, counterions (Li⁺, Na⁺, K⁺, Mg²⁺) always remain in the bisector plane of the O1-P-O2 angle. When these counterions are explicitly hydrated, the smallest counterions (Li⁺, Na⁺) deviate from the bisector plane, while the largest counterions (K⁺ and Mg²⁺) always remain in the same plane. On the other hand, the present calculations reveal that the g⁺g⁺ conformer is the most stable in the presence of monovalent counterions, while conformers g⁺t and g^-t are the most stable in the presence of the divalent counterion Mg²⁺. Finally, the hybrid solvation model seems to be in better agreement with the available crystallographic and spectroscopic (Raman) experiments than the explicit model. Indeed, the six conformational torsions of the C4'-C3'-O3'-PO^-₂-O5'-C5'-C4' segment of all complexes of the g^-g^- conformer in 6H₂O/Continuum remain similar to the available experimental data of A- and B-DNA forms. The calculated wavenumbers of the g⁺g⁺ conformer in the presence of the monovalent counterion and of g^-t conformer in presence of the divalent counterion in the hybrid model are in good agreement with the Raman experimental data of A- and B-DNA forms. In addition, the maximum deviation between the calculated wavenumbers in the 6H₂O/Continuum for the g⁺g⁺ conformer and experimental value measured in an aqueous solution of the DMP-Na⁺ complex, is <1.07% for the PO₂^- (asymmetric and symmetric) stretching modes and <2.03% for the O5'-C5' and O3'-C3' stretching modes. Graphical abstract dDSMP-(OO)^- Mg²⁺/6W/Continuum.

DFT study of the effect of solvent on the H-atom transfer involved in the scavenging of the free radicals (·)HO2 and (·)O2(-) by caffeic acid phenethyl ester and some of its derivatives

H-atom transfer from caffeic acid phenethyl ester (CAPE), MBC (3-methyl-2-butenyl caffeate), BC (benzoic caffeate), P3HC (phenethyl-3-hydroxycinnamate), and P4HC (phenethyl-4-hydroxycinnamate) to the selected free radicals (·)HO2 and (·)O2(-) was studied. Such a transfer can proceed in three different ways: concerted proton-coupled electron transfer (CPCET), electron transfer followed by proton transfer (ET-PT), and proton transfer followed by electron transfer (PT-ET). The latter pathway is sometimes competitive with SPLET (sequential proton loss electron transfer) in polar media. Analyzing the thermodynamic descriptors of the reactions of CAPE and its derivatives with co-reactive species-in particular, the free energies of reactions, the activation barrier to the CPCET mechanism, and their rate constants-appears to be the most realistic method of investigating the H-atom transfers of interest. These analyses were performed via DFT calculations, which agree well with the data acquired from experimental studies (IC50) and from CBS calculations. The CPCM solvation model was used throughout the work, while the SMD model-employed as a reference-was used only for CAPE. The main conclusion drawn from the analysis was that SPLET is the mechanism that governs the reaction of phenolic acids with (·)HO2, while PT-ET governs the reaction of phenols with (·)O2(-). In kinetic investigations of the CPCET process, the rate constant decreases as the solvent polarity increases, so the reaction velocity slows down.

Solvation Energies of the Proton in Methanol

pKa's, proton affinities, and proton dissociation free energies characterize numerous properties of drugs and the antioxidant activity of some chemical compounds. Even with a higher computational level of theory, the uncertainty in the proton solvation free energy limits the accuracy of these parameters. We investigated the thermochemistry of the solvation of the proton in methanol within the cluster-continuum model. The scheme used involves up to nine explicit methanol molecules, using the IEF-PCM and the strategy based on thermodynamic cycles. All computations were performed at B3LYP/6-31++G(dp) and M062X/6-31++G(dp) levels of theory. It comes out from our calculations that the functional M062X is better than B3LYP, on the evaluation of gas phase clustering energies of protonated methanol clusters, per methanol stabilization of neutral methanol clusters and solvation energies of the proton in methanol. The solvation free energy and enthalpy of the proton in methanol were obtained after converging the partial solvation free energy of the proton in methanol and the clustering free energy of protonated methanol clusters, as the cluster size increases. Finally, the recommended values for the solvation free energy and enthalpy of the proton in methanol are -257 and -252 kcal/mol, respectively.

Vibrational analysis of amino acids and short peptides in hydrated media. IV. Amino acids with hydrophobic side chains: L-alanine, L-valine, and L-isoleucine

In the framework of our investigations on the analysis of vibrational spectra of amino acids (AAs) in hydrated media, Raman scattering and Fourier transform infrared (FT-IR) attenuated transmission reflectance (ATR) spectra of three alpha-amino acids with hydrophobic hydrocarbon side chains, i.e., alanine, valine, and isoleucine, were measured in H2O and D2O solutions. The present data complete those recently published by our group on glycine and leucine. This series of observed vibrational data gave us the opportunity to analyze the vibrational features of these amino acids in hydrated media by means of the density functional theory (DFT) calculations at the B3LYP/6-31++G* level. Harmonic vibrational modes calculated after geometry optimization on the clusters containing five water molecules interacting with H-donor and H-acceptor sites of amino acids are performed and allowed the observed main Raman and infrared bands to be assigned. Additional calculations on a cluster formed by leucine (L) and five water (W) molecules and the comparison of the obtained data with those recently published by our group on L+12W, allowed us to justify the number of hydration considered in the present report.

Geometrical and vibrational features of phosphate, phosphorothioate and phosphorodithioate linkages interacting with hydrated cations: a DFT study

The effect of hexahydrated monovalent and divalent cations on the geometrical and vibrational features of dimethyl phosphate, dimethyl phosphorothioate and dimethyl phosphorodithioate anions (simple suitable model compounds representing the anionic moieties of natural and some modified nucleic acids) was studied. For this purpose, density functional theory (DFT) calculations were carried out at the B3LYP/6-31++G* level. Our results indicate that only K(+) and Mg(2+) prefer to be located in the bisector plane of the PO(2)(-) angle, whereas Li(+) and Na(+) deviate from this plane. Monovalent and divalent cations are slightly deviated from the OPS(-) bisector plane and are found closer to the free oxygen atom. Moreover, the present calculations have shown that in contrast to the general belief, the g(-)g(-) conformer (with respect to the torsion angles defined around the P-O ester bonds) is not always the energetically most favorable. For instance, the g(-)t conformer presents the lowest energy in the case of dimethyl phosphorothioate. The calculated vibrational wavenumbers obtained for dimethyl phosphate and dimethyl phosphorothioate interacting with hydrated sodium counterion, were compared with those previously recorded by Raman scattering and infrared absorption (IR) in aqueous solutions. It has been evidenced that the use of explicit solvent versus dielectric continuum, considerably improves the agreement between the theoretical and observed characteristic wavenumbers.