6-31G Level Research Articles

Impact of solvation on the geometrical parameters of some amino acids

The impact of the utilized solvent is of an important concern. Eliminating the effect of solvents and other factors is a crucial point in order to get more accurate results. Therefore, density functional theory DFT calculations at B3LYP/ 6-31G(d,p) level were carried out for a number of amino acids in the gaseous state and also under the effect of various solvation processes using different solvents; DMSO, acetonitrile (AN), nitromethane (NM) and methanol (Meth). Geometrical parameters of both N and C terminals were investigated. Results demonstrate that different solvation processes affect the studied parameters that should be considered for future applications.

Predictive Modeling of the Human Hepatoma (Huh-7D12) Cancer Line of a Series of bis- (5-arylidene-rhodanine-3-yl) Diamine

This work deals with the prediction of the antiproliferative activity of eighteen (18) substances derived from bis-5-arylidene rhodanine against human hepatoma tumor line (Huh-7D12). By applying the functional density theory (DFT) method to the B3LYP / 6-31G (d, p) level, theoretical descriptors were determined and correlated with antiproliferative (Huh-7) activity by linear regression multiple (RML). This correlation has shown that the electron energy, the energy of the lowest vacant molecular orbital (ELUMO) and the molecular volume (VM) are the quantum and geometric descriptors that best influences the antiproliferative activity of the molecules studied. The coefficient of determination R2 indicates that 97.9% of the molecular descriptors defining this model are taken into account with a standard deviation of 0.015. The significance of the model reflected by the Fischer test is estimated at 123.648. The robustness of the model given by the cross-validation correlation coefficient (Q2CV) is 97.9%. This model has been validated by Tropsha criteria. The very good correlation between these three descriptors and the Huh-7 activity was confirmed by the nonlinear multiple regression (RNML) method with better statistical data. (R2 = 0,998 ; Q2CV = 0,998 ; RMSE = 0,006).

Electron Donor and Acceptor Influence on the Nonlinear Optical Response of Diacetylene-Functionalized Organic Materials (DFOMs): Density Functional Theory Calculations.

Herein, we report the quantum chemical results based on density functional theory for the polarizability (α) and first hyperpolarizability (β) values of diacetylene-functionalized organic molecules (DFOM) containing an electron acceptor (A) unit in the form of nitro group and electron donor (D) unit in the form of amino group. Six DFOM 1–6 have been designed by structural tailoring of the synthesized chromophore 4,4′-(buta-1,3-diyne-1,4-diyl) dianiline (R) and the influence of the D and A moieties on α and β was explored. Ground state geometries, HOMO-LUMO energies, and natural bond orbital (NBO) analysis of all DFOM (R and 1–6) were explored through B3LYP level of DFT and 6-31G(d,p) basis set. The polarizability (α), first hyperpolarizability (β) values were computed using B3LYP (gas phase), CAM-B3LYP (gas phase), CAM-B3LYP (solvent DMSO) methods and 6-31G(d,p) basis set combination. UV-Visible analysis was performed at CAM-B3LYP/6-31G(d,p) level of theory. Results illustrated that much reduced energy gap in the range of 2.212–2.809 eV was observed in designed DFOM 1–6 as compared to parent molecule R (4.405 eV). Designed DFOM (except for 2 and 4) were found red shifted compared to parent molecule R. An absorption at longer wavelength was observed for 6 with 371.46 nm. NBO analysis confirmed the involvement of extended conjugation and as well as charge transfer character towards the promising NLO response and red shift of molecules under study. Overall, compound 6 displayed large <α> and βtot, computed to be 333.40 (a.u.) (B3LYP gas), 302.38 (a.u.) (CAM-B3LYP gas), 380.46 (a.u.) (CAM-B3LYP solvent) and 24708.79 (a.u.), 11841.93 (a.u.), 25053.32 (a.u.) measured from B3LYP (gas), CAM-B3LYP (gas) and CAM-B3LYP (DMSO) methods respectively. This investigation provides a theoretical framework for conversion of centrosymmetric molecules into non-centrosymmetric architectures to discover NLO candidates for modern hi-tech applications.

Binding of histidine and proline with graphene: DFT study

M06-2X/6-31G(d) level calculations were performed to examine the interactions of two α-amino acids (histidine and proline) individually with two finite-sized graphene sheets (C62H20 and C186H36). The conformers and orientations of histidine and proline on the surface of graphene play an important role in determining the stabilities of complexes. The number and type of non-bonding interactions such as π-π, CH⋯π, NH⋯π and OH⋯π account for the stabilization of the complexes. The binding energy in aqueous phase generally decreases compared to gas phase. HOMO-LUMO energy gap of graphene is not altered by binding of either proline or histidine.

Computational studies on [4 + 2] / [3 + 2] tandem sequential cycloaddition reactions of functionalized acetylenes with cyclopentadiene and diazoalkane for the formation of norbornene pyrazolines.

The mechanistic pathways for the sequential tandem [4 + 2] / [3 + 2] versus [3 + 2] / [4 + 2] cycloaddition reaction of functionalized acetylenes with cyclopentadiene and dimethyl diazopropane for the formation of norbornene pyrazolines, employed in the synthesis of pharmaceutically relevant compounds, have been studied computationally with DFT at the M06-2X/6-31G(d) and M06-2X/6-31G(d,p) levels of theory. We have established that, in the reaction of the parent (unsubstituted) acetylene with cyclopentadiene and dimethyl diazopropane, the order of the tandem addition has no substantial effects in product outcomes. The same product is obtained provided the reaction components remain the same for both [4 + 2]/[3 + 2] and [3 + 2]/[4 + 2] tandem addition sequences. The results indicate that the [4 + 2] Diels-Alder addition step is the rate-determining step irrespective of the addition order, while the 1,3-dipolar cycloaddition step has been found to generally proceed rapidly with very low activation energies. It has also been realized that the regio-, stereo-, and chemo-selectivities of the reaction are strictly dictated by the type of substituent on the parent acetylene. For substituted acetylenes, we conclude that the sequence of the tandem addition generally affects the type of isomeric product obtained. The [4 + 2]/[3 + 2] tandem addition sequence has been established to favor the exo stereo-selective isomer over the endo, whereas the [3 + 2]/[4 + 2] tandem addition sequence generally favors the endo product formation. Therefore, it is settled that the mechanistic route taken by any substrate in the [4 + 2]/[3 + 2] versus [3 + 2]/[4 + 2] sequential tandem cycloaddition is greatly affected by both electronic and steric factors. Electrophilicity indices calculations agree with the activation barriers obtained. Perturbation molecular orbital theory was employed to rationalize the results. Global reactivity indices calculations gave a good correlation with the activation energies. Graphical abstract The sequential tandem [4 + 2] / [3 + 2] versus [3 + 2] / [4 + 2] cycloaddition reaction of functionalized acetylenes with cyclopentadiene and dimethyl diazopropane for the formation of norbornene pyrazolines.

Electrochemical oxidation of 2,5-diethoxy 4-morpholinoaniline in the presence of thiobarbituric acid: present an ECCCEC Mechanism

The electrochemical oxidation of 2,5-diethoxy-4-morpholinoaniline has been studied in the presence of thiobarbituric acid by the use of experimental and calculation methods. Cyclic voltammetry, controlled-potential coulometry and density functional theory (DFT) were used in this study. By the use of the cyclic voltammetry, the best condition of synthesis was obtained, and controlled-potential coulometry was performed under this condition. The results indicated that the produced p-benzoquinonediimine is unstable, and it was hydrolyzed in the experimental condition. It was found that the produced p-quinoneimine from oxidation/hydrolysis of 2,5-diethoxy-4-morpholinoaniline reacts with the thiobarbituric acid as a nucleophile and via an ECCCEC mechanism converts to the product. Also, computational calculations were used to analyze oxidation peaks in voltammetry. DFT, BP86 level of theory and 6-31G(p,d) basis set, was used to obtain the theoretical results.

Nature of interlayer carbon–carbon covalent bonding in graphene-based materials

This study provides a fundamental understanding of the nature of C–C interlayer covalent bonding in graphene-based materials by using the dispersion-corrected density functional theory B3LYP-D3/6-31+G(2df,p)//B3LYP-D3/6-31G(d,p) (single-point energies at the larger 6-31+G(2df,p) basis set using fully optimized geometries at the B3LYP-D3/6-31G(d,p) level). With a bilayer hydrogenated graphene model, a partial covalent bonding was found upon dehydrogenation from opposite layers between interior carbon atoms even at the distance of greater than 4.00 A. To facilitate such bonding carbon atoms must transform from its sp3 to sp2 hybridization upon dehydrogenation so that pz orbitals can extend farther for better overlap at a large distance. The structure containing a single partial covalent bond was found to be less stable compared to its nonbonding triplet state. However, adding normal interlayer covalent bonds at the edge helps to stabilize such partial bond. In addition, forming a partial interlayer covalent bond greatly reduces band gap to 1 eV, whereas the formation of a normal covalent bond causes only a slight change in the band gap. Thus, controlling the population of the two types of interlayer bonds can, therefore, open up a promising way to control the band gap for organic semiconductor materials.

Predictive Modeling of Breast Anticancer Activity of a Series of Coumarin Derivatives using Quantum Descriptors

We focused on a series of coumarin derivatives in this work. The method of Density Functional Theory (DFT) of quantum chemistry has been used at B3LYP / 6-31G (d, p) level in order to identify molecular descriptors which are useful for this study. The analysis of the statistical indicators allowed to obtain a QSAR model based on quantum descriptors and anti-cancer activity against breast cancer (MCF-7) that were accredited for good statistical performance. For the model, the statistical indicators were: correlation coefficient R2 = 0.904, standard deviation S = 0.102, Fischer test coefficient F = 18.779 and correlation coefficient of cross validation

Investigation of spectroscopic studies and DFT calculations on glucofuranose derivatives of dithiophosphonates

2,4-Bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane-2,4-disulfide (Lawesson’s reagent: LR) was reacted with 1,2:5,6-di-O-cyclohexylidene-α-D-glucofuranose and 1,2:5,6-di-O-isopropylidene-α-D-glucofuranose in toluene and gave rise to crude dithiophosphonic acids. The crude dithiophosphonic acids were treated with excess triethylamine and the triethylammonium salts of dithiophosphonic acids (1) and (2) were isolated by crystallization method. Compounds 1 and 2 were characterized by elemental analysis, IR, and NMR (1H-, 13C- and 31P-) spectroscopies and mass spectrometry. In addition, NMR spectra, the electronic properties (the electronic chemical potential, electronegativity, chemical hardness and the global electrophilicity index) and NBO analysis of compound 2 have been calculated by using the Gaussian 16 W program. The electronic properties were calculated using Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) energies by density functional method (DFT/B3LYP) at 6-31G(d,p) level. The HOMO and LUMO energies are −5.9 and −0.72 eV, respectively. The HOMO–LUMO energy difference is 5.18 eV and this value shows that compound 2 has a high stability and low reactivity.

Excited State Frequencies of Chlorophyll f and Chlorophyll a and Evaluation of Displacement through Franck-Condon Progression Calculations.

We present ground and excited state frequency calculations of the recently discovered extremely red-shifted chlorophyll f. We discuss the experimentally available vibrational mode assignments of chlorophyll f and chlorophyll a which are characterised by particularly large downshifts of 131-keto mode in the excited state. The accuracy of excited state frequencies and their displacements are evaluated by the construction of Franck–Condon (FC) and Herzberg–Teller (HT) progressions at the CAM-B3LYP/6-31G(d) level. Results show that while CAM-B3LYP results are improved relative to B3LYP calculations, the displacements and downshifts of high-frequency modes are underestimated still, and that the progressions calculated for low temperature are dominated by low-frequency modes rather than fingerprint modes that are Resonant Raman active.

Natural dye extract from Cassia fistula and its application in dye-sensitized solar cell: Experimental and density functional theory studies

Natural dye extracted from Cassia fistula (C. fistula) flower is used as photosensitizer to fabricate titanium dioxide (TiO2) based dye-sensitized solar cells (DSSC). Ethanol was used as the extracting solvent. Kaempferol, Leucopelarrgonidin and Rhein are the major pigments present in C. fistula. The optimized molecular structure for these constituents were obtained using density functional theory (DFT) at 6-31G(d,p) level. The HOMO–LUMO analysis was performed to study the energy-gap using optimized structure. All the calculations were performed in the gas phase and taking ethanol as solvent. The electron transfer characteristics between the dye's lowest unoccupied molecular orbital (LUMO) and the conduction band of TiO2 were studied. The photoelectric parameters Voc = 0.549 V, Jsc = 0.51 mA/cm2 and η = 0.21% were obtained with DSSC fabricated using C. fistula-sensitized TiO2 photo anode under 100 mW/cm2 illumination.

Conformation dependence of tyrosine binding on the surface of graphene: Bent prefers over parallel orientation

Binding of tyrosine (Tyr) with two finite size graphene sheets of 62 and 186 carbon atoms was investigated using M06-2X/6-31G(d) level. Thorough conformational analysis was done for tyrosine to select few conformers to explore their complexation by considering different orientations on the surface of graphene. The binding energy values are not significantly changed while moving from small to large graphene. Tyrosine exhibits strong π-π interactions that support recent experiments on binding of aromatic amino acids on the surface of graphene and modified graphene. The binding energies of 9.4–9.9 kcal/mol were obtained for different conformers of tyrosine binding with graphene via parallel orientation (having π-π and C(β)-H…π interactions). Owing to multiple interactions including C-H…π, N-H/O-H…π and π-π, the bent prefers over parallel orientation (by 1 kcal/mol) for the high energy conformer of Tyr adsorption on graphene. The binding energies in the aqueous medium are slightly lower than those obtained in the gas phase. HOMO-LUMO energy gaps calculated at the TPSSh/6-31G(d) level suggest that adsorption of tyrosine conformers with different orientations on the surface of graphene does not affect the band gap value of graphene (1.43 and 0.08 eV correspondingly for small and large graphene). Intermolecular orbital interactions support the π-π interactions in bent and parallel orientations of tyrosine with graphene.

Gas-Phase Reactions of the Group 10 Organometallic Cations, [(phen)M(CH3)]+ with Acetone: Only Platinum Promotes a Catalytic Cycle via the Enolate [(phen)Pt(OC(CH2)CH3)]+

Abstract Electrospray ionisation of the ligated group 10 metal complexes [(phen)M(O2CCH3)2] (M = Ni, Pd, Pt) generates the cations [(phen)M(O2CCH3)]+, whose gas-phase chemistry was studied using multistage mass spectrometry experiments in an ion trap mass spectrometer with the combination of collision-induced dissociation (CID) and ion-molecule reactions (IMR). A new catalytic cycle has been discovered. In step 1, decarboxylation of [(phen)M(O2CCH3)]+ under CID conditions generates the organometallic cations [(phen)M(CH3)]+, which react with acetone to generate the [(phen)M(CH3)(OC(CH3)2)]+ adducts in competition with formation of the coordinated enolate for M = Pt (step 2). For M = Ni and Pd, the adducts regenerate [(phen)M(CH3)]+ upon CID. In the case of M = Pt, loss of methane is favored over loss of acetone and results in the formation of the enolate complex, [(phen)Pt(OC(CH2)CH3)]+. Upon further CID, both methane and CO loss can be observed resulting in the formation of the ketenyl and ethyl complexes [(phen)Pt(OCCH)]+ and [(phen)Pt(CH2CH3)]+ (step 3), respectively. In step 4, CID of [(phen)Pt(CH2CH3)]+ results in a beta-hydride elimination reaction to yield the hydride complex, [(phen)Pt(H)]+, which reacts with acetic acid to regenerate the acetate complex [(phen)Pt(O2CCH3)]+ and H2 in step 5. Thus, the catalytic cycle is formally closed, which corresponds to the decomposition of acetone and acetic acid into methane, CO, CO2, ethene and H2. All except the last step of the catalytic cycle are modelled using DFT calculations with optimizations of structures at the M06/SDD 6-31G(d) level of theory.

Theoretical Study on Criegee Intermediate's Role in Ozonolysis of Acrylic Acid.

Criegee intermediates have raised much attention in atmospheric chemistry because of their significance in ozonolysis mechanism. The simplest Criegee intermediate, CH2OO, and its reactions with acrylic acid including cycloadditions and insertions as main entrance channels have been investigated at CCSD(T)/cc-pVTZ//M06-2X/6-31G(d,p) level. Temperature- and pressure-dependent kinetics were predicted by solving the time-dependent master equations based on Rice-Ramsperger-Kassel-Marcus theory using MESS program, with temperatures from 200 to 500 K and pressures from 0.001 to 1000 atm. Variational transition state theory (VTST) was used for barrierless pathways and conventional transition state theory (CTST) for pathways with distinct barriers. Results indicate that hydroperoxymethyl acrylate is the dominant product under atmospheric conditions. The combination of two reactants will reduce the volatility and makes a possible factor that induces formation of secondary organic aerosols, which suggests CH2OO's entangled role in ever-increasing air pollution.

Application of metallofullerene towards adsorption of mustard gas: a detailed DFT study

Towards investigation on the application of metallofullerene in the removal of mustard gas, a fullerene C20 has been considered for substitutional doping by three of transition metals (Ti, Fe, and Ni). The resulted metallofullerenes (C19Ti, C19Fe, and C19Ni) were considered for the interaction of mustard gas in its surface by using DFT calculations in B3LYP-D3/631G (d,p) level of theory. We used NBO and frontier molecular orbital (FMO) techniques to track the change in the electronic structure of metallofullerenes upon mustard gas adsorption. During adsorption of mustard gas, the direction of charge transfer is from mustard to clusters which points towards p-type conduction property of metallofullerenes. Our results reveal that the metallofullerene may be an ideal candidate for the adsorption of mustard gas with adsorption energies in the range of − 96 to − 102 kJ/mol.

A pH-Switchable Electrostatic Catalyst for the Diels-Alder Reaction: Progress toward Synthetically Viable Electrostatic Catalysis.

Density functional theory calculations at the SMD/M06-2X/6-31+G(d,p)//M06-2X/6-31G(d) level of theory have been used to computationally design and test a pH-switchable electrostatic organocatalyst for Diels-Alder reactions. The successful catalyst design, bis(3-(3-phenylureido)benzyl)ammonium, was studied for the reaction of p-quinone with range of cyclic, heterocyclic, and acyclc dienes and also the reaction of cyclopentadiene with maleimide and N-phenylmaleimide. All reactions showed significant enhancements in catalysis (10-32 kJ mol-1 in barrier lowering) when the catalyst was protonated, consistent with electrostatic stabilization of the transition state. Electrostatic effects were found to diminish in polar solvents but were predicted to remain significant in nonpolar solvents.

A Fragment Quantum Mechanical Method for Metalloproteins.

An accurate energy calculation of metalloprotein is of crucial importance and also a theoretical challenge. In this work, a metal molecular fractionation with conjugate caps (metal-MFCC) approach is developed for efficient linear-scaling quantum calculation of potential energy and atomic forces of metalloprotein. In this approach, the potential energy of a given protein is calculated by a linear combination of potential energies of the neighboring residues, two-body interaction energy between non-neighboring residues that are spatially in close contact and the potential energy of the metal binding group. The calculation of each fragment is embedded in a field of point charges representing the remaining protein environment. Numerical studies were carried out to check the performance of this method, and the calculated potential energies and atomic forces all show excellent agreement with the full system calculations at the M06-2X/6-31G(d) level. By combining the energy calculation with molecular dynamic simulation, we performed an ab initio structural optimization for a zinc finger protein with high efficiency. The present metal-MFCC approach is linear-scaling with a low prefactor and trivially parallelizable. The individual fragment typically contains about 50 atoms, and it is thus possible to be calculated at higher levels of the quantum chemistry method. This fragment method can be routinely applied to perform structural optimization and ab initio molecular dynamic simulation for metalloproteins of any size.

Experimental and Computational Study of the Gas-Phase Acidities of Acidic Di- and Tripeptides.

Gas-phase acidities (GA or Δ Gacid) of acidic di- and tripeptides are determined for the first time. The peptides studied are composed of inert alanine (A) residues and one X residue of either aspartic acid (D) or glutamic acid (E): AX, XA, AAX, AXA, and XAA. Experimental GAs were measured by the thermokinetic method of deprotonation ion/molecule reactions in a Fourier transform ion cyclotron resonance mass spectrometer. Calculated GAs were obtained by composite correlated molecular orbital theory at the G3(MP2) level for deprotonation of carboxylic acid groups both at the C-terminus and at the side chain. Excellent agreement was found between experimental and calculated GA values. There is a slight preference for peptides with D being more acidic than analogous peptides with E, which agrees with the GAs of the corresponding amino acids. Experiments showed that peptides are more acidic (lower numerical GA values) when the acidic residue is located at the C-terminus (i.e., AX or AAX). The lowest energy form of deprotonated AAE has a unique structure where the longer side chain of E allows the two carboxylates, which are in close proximity, to share the proton. The tripeptides are less acidic (higher GA value) by 3-7 kcal/mol when the acidic residue is in the center. The tripeptides are more acidic (by 2-10 kcal/mol) than dipeptides containing the same acidic residue at the same location.

Insights into the reaction mechanism of n-hexane dehydroaromatization to benzene over gallium embedded HZSM-5: effect of H2 incorporated on active sites.

The catalytic dehydroaromatization of alkanes to aromatics has attracted considerable attention from the scientific community, because it can be used for the upgrading of low-cost alkanes into high added-value aromatics, such as benzene, toluene, and xylene (BTX). In this context, we report the reaction mechanism of n-hexane dehydroaromatization to benzene over two different reduced gallium species embedded in HZSM-5, including univalent Ga+ embedded in HZSM-5 (Ga/HZSM-5) and dihydrido gallium complex (GaH2+) embedded in HZSM-5 (GaH2/HZSM-5) by using the M06-2X/6-31G(d,p) level of calculation. The reaction proceeds by following two main steps: (i) the dehydrogenation of hexane to haxa-1,3,5-triene; (ii) the dehydroaromatization of haxa-1,3,5-triene to benzene. For the univalent Ga+ embedded in HZSM-5, the first step of the hexane dehydrogenation is considered to be the rate-determining step, which requires a high activation energy of 76.6 kcal mol-1. In strong contrast to this, in the case of the GaH2/HZSM-5 catalyst the rate determining step is found to be the second hydrogen abstraction from n-hexane with a lower activation barrier of 11.1 kcal mol-1. The reaction is therefore preferentially taking place over the GaH2/HZSM-5 catalyst. These observations clearly confirm the existence of a dihydrido gallium complex (GaH2+) as one of the most active species for the dehydroaromatization of alkanes and it is obtained in the presence of hydrogen in the catalytic system. This example opens up perspectives for a better understanding of the effect of active species on the catalytic reaction.

One-photon Absorption Characterizations, Dipole Polarizabilities and Second Hyperpolarizabilities of Chlorophyll a and Crocin

Abstract The dispersion-free dipole polarizability (α) computations for chlorophyll a (1) and crocin (2) have been achieved by density functional theory (DFT) at B3LYP/ 6-31G(d) level. The measured one-photon absorption (OPA) wavelengths are quite consistence with the theoretically obtained values. Ab-initio quantum chemical calculations (time-dependent Hartree-Fock (TDHF)) have been implemented to reveal the static second hyperpolarizabilities (γ) and dynamic dipole polarizabilities of the title molecules. The examined compounds display γ with non-zero values, introducing their third-order nonlinear optical (NLO) phenomena. The first and second frontier molecular orbitals of the investigated molecules have been also derived from DFT.