B3LYP Level Of Theory Research Articles

Intramolecular Interactions versus Hydration Effects on p-Guanidinoethyl-phenol Structure and pKa Values

We analyze the structure, hydration, and pK(a) values of p-guanidinoethyl-phenol through a combined experimental and theoretical study. These issues are relevant to understand the mechanism of action of the tetrameric form, the antibacterial compound tetra-p-guanidinoethyl-calix[4]arene (Cx1). The investigated system can also be useful to model other pharmaceutical drugs bearing a guanidine function in the vicinity of an ionizable group and the effect of arginine on the pK(a) of vicinal ionizable residues (in particular tyrosine) in peptides. The p-guanidinoethyl-phenol monomer (mCx1) has two ionizable groups. One important particularity of this system is that it exhibits high molecular flexibility that potentially leads to enhanced stabilization in folded structures by direct, strong Coulombic interactions between the ionizable groups. The first pK(a) corresponding to ionization of the -OH group has experimentally been shown to be only slightly different from usual values in substituted phenols. However, because of short-range Coulombic interactions, the role of intramolecular interactions and solvation effects on the acidities of this compound is expected to be important and it has been analyzed here on the basis of theoretical calculations. We use a discrete-continuum solvation model together with quantum-mechanical calculations at the B3LYP level of theory and the extended 6-311+G(2df,2p) basis set. Both intra- and intermolecular effects are very large (~70 kcal/mol) but exhibit an almost perfect compensation, thus explaining that the actual pK(a) of mCx1 is close to free phenol. The same compensation of environmental effects applies to the second pK(a) that concerns the guanidinium group. Such a pK(a) could not be determined experimentally with standard titration techniques and in fact the theoretical study predicts a value of 14.2, that is, one unit above the pK(a) of the parent ethyl-guanidinium molecule.

A DFT Study on the Cycloaddition of Dimethyl Acetylenedicarboxylate and 3,4-dihydroisoquinoline-N-oxide

A theoretical study of the kinetics and mechanism of the second-order intermolecular cycloaddition of dimethyl acetylenedicarboxylate and [3,4-dihydroiso-quinoline-N-oxide] was performed using DFT methods at B3LYP levels of theory with a 6-311G (d,p) basis set at 298.15 K. Equilibrium molecular geometries and harmonic vibrational frequencies of the reactants, transition state and product were calculated. The effect of solvent on the kinetic and thermodynamic parameters of the reaction were investigated. The calculated rate constants and activation parameters showed good agreement with experimental results. These calculations indicated that the reaction proceeds through a synchronous concerted mechanism.

Quantum chemical investigation of the intra- and intermolecular proton transfer reactions and hydrogen bonding interactions in 4-amino-5-(2-hydroxyphenyl)-2H-1,2,4-triazole-3(4H)-thione

The intramolecular thione-thiol tautomerism and intermolecular double proton transfer reaction of the hydrogen-bonded thione and thiol dimers in the title triazole compound were studied at the B3LYP level of theory using 6-311++G(d,p) basis function. The influence of the solvent on the single and double proton transfer reactions was examined in three solvents (chloroform, methanol and water) using the polarizable continuum model (PCM) approximation. The computational results show that the thione tautomer is the most stable isomer with a very high tautomeric energy barrier both in the gas phase and in solution phase, indicating a quite disfavored process. The solvent effect is found to be sizable with increasing polarity. In the double proton transfer reaction, the thione dimer is found to be more stable than thiol dimer both in the gas phase and in solution phase. The energetic and thermodynamic parameters of the double proton transfer process show that the double proton exchange from thione dimer to thiol dimer is thermodynamically unfavored. However, the exchange from thiol dimer to thione dimer for the gas phase and water phase seems to be feasible with a low barrier height and with a negative value in enthalpy and free energy changes. In addition, the hydrogen bonding interactions were analyzed in the gas phase regarding their geometries and energies. It is found that all complex formations are enthalpically favored, and the stability of the H-bonds comes in the order of S1-H2···N2>N2-H2···S1>N3-H3B···O1. Finally, non-linear optical properties were carried out at the same calculation level in the gas phase.

Cooperative effects of noncovalent bonds to the Br atom of halogen-bonded H3N…BrZ and HCN…BrZ (Z = F, Br) complexes

A series of complexes formed between halogen-bonded H(3)N/HCN...BrZ (Z = Br, F) dimers and H(3)N/HCN...BrZ...XY (XY = HF, ClF, BeH(2), LiF) trimers were investigated at the MP2 and B3LYP levels of theory using a 6-31++G(d,p) basis set. Optimized structures, interaction energies, and other properties of interest were obtained. The addition of XY to the H(3)N/HCN...BrZ dyad leads to enhanced intermolecular binding with respect to the isolated monomers. This enhanced binding receives contributions from the electrostatic and inductive forces between the constituent pairs, with, in some instances, substantial three-body non-additive contributions to the binding energy. It was found that the XY = LiF interaction causes the greatest distortion of the H(3)N/HCN...BrZ halogen bond from the preferred linear orientation and also provides the strongest binding energy via the nonadditive energy.

Ab initio study on the intermolecular interactions between 1,1-diamino-2,2-dinitroethylene and acetylene: Pull effect on complex formation

The (1:1) complexes of 1,1-diamino-2,2-dinitroethylene (FOX-7) with acetylene were studied computationally. The structure of the complexes, energies and the vibrational frequencies were computed at the HF and B3LYP levels of theory using 6-31G**, 6-311G**, 6-31++G** and 6-311++G** basis sets. The 1A type structure is most stable structure corresponding to N–H⋯π complex of FOX-7-acetylene. The ZPE+BSSE corrected binding energy for 1A is predicted to be −2.01kcal/mol at the B3LYP/6-311++G** level. To understand the pull effect on complex formation, the most stable 1A type structure were searched in 1,1-diamino-2-nitroethylene (DANE)-acetylene and 1,1-diaminoethylene (DAE)-acetylene complexes using HF and B3LYP levels using a 6-311++G** basis set. The 1E structure of DANE-acetylene complex is quite similar to the most stable structure of FOX-7-acetylene (1A). The absence of electron-withdrawing nitro groups in DAE results in the transformation of the structure, which makes the absence of N–H⋯π hydrogen bond in DAE(1)-acetylene. AIM analysis was also performed to understand the nature of the interactions in these complexes.

Electronic structure study of the triplet azulene-like molecules

In this Letter a detailed electronic structure study of singlet and triplet states of a series of azulene-like molecules was performed using several DFT and complete active space (CAS) methods. According to the results obtained at the B3LYP level of theory using the unrestricted symmetry-broken method, the singlet–triplet splitting for the members of the series with three and more hexagons is quite small, and in addition, four members of the series were found to be triplet diradicals. The CASSCF calculations revealed that higher members of the series of the azulene-like molecules with six and more hexagons are triplet diradicals.

A THEORETICAL STUDY OF DACTYLYNE STEREOISOMERS: A MARINE NATURAL PRODUCT FROM APLYSIA DACTYLOMELA

Dactylyne is an acetylenic dibromochloro ether from the Persian Gulf sea hare, Aplysia dactylomela. As a result of its unique structure and nontoxic nature; it has been known as a promising pharmacological substance of marine origin. A theoretical study of dactylyne and its stereoisomers, initiated in the hope of understanding more details of its action, is reported here. In the present research, for the first time, a density functional theory (DFT) calculation has been performed on the stereoisomers of dactylyne to determine the most stable configurations in gas phase. The HOMO–LUMO gap, global softness, chemical potential, and electrophilicity index have been calculated for the most stable stereoisomers at the B3LYP level of theory. These DFT-based global reactivity descriptors have been applied to demonstrate the reactive nature of compounds. Moreover, results from the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis have been employed to support the finding of more reactive stereoisomers. The investigation has indicated that the configuration of stereoisomers has some effects on their electronic and structural properties which control their global reactivity. It is also shown that the most probable interaction sites of dactylyne are in its unsaturated region. In the second part of our study, the effects of some typical substituents on dactylyne reactivity have been investigated theoretically and it has been shown that the strong electron donor groups increase the reactivity of dactylyne more than withdrawing substituent. However, creation of an ionic compound highly influences on reactivity descriptors.

Nonclassical hydrides of Ni+ in ZSM-5 zeolite structures: A hybrid DFT study

We have studied the reactivity towards dihydrogen of Ni2+–Ni+ reduced ions, residing above two framework oxygen atoms, using a 18 SiO4 tetrahedrals (18T) model cluster representing the intersection of the straight and the sinusoidal channels in ZSM-5 zeolite. Reported are a detailed analysis of the Ni+–H2 orbital interactions, the thermodynamic stability, and characteristic spectral signatures of the predicted Ni+(H2)n nonclassical hydrides for n=1 and 2, at the B3LYP level of theory. Comparison is made to existing spectroscopy data for a Ni+(H2) complex formed in Ni-exchanged ZSM-5 zeolite [11].

Synthesis and computational study of two new glycoluril clips containing benzocrown ether side walls

Two new glycoluril-derived molecular clips containing benzocrown ether side walls have been synthesized via reaction of a glycoluril scaffold with two bromomethylated benzocrown ethers. The molecular geometry of their most stable structures were investigated with density functional theory at the B3LYP level of theory using STO-3G, 6-31G, and 6-311G basis sets. Then based on the obtained computer-optimized structures, the binding properties of one clip with some 5-substituted resorcinols have been calculated.

Quantum chemical investigation on the reaction mechanism of tertiary phosphines with unsaturated carboxylic acids: An insight into kinetic data

AbstractThe structures of intermediates and transition states in the reaction of tertiary phosphines with unsaturated carboxylic acids have been calculated at the B3LYP level of theory using the 6‐31+G(d,p) basis set. Analysis of the results shows that [1,3]‐intramolecular migration of carboxylic proton to carbanionic center of generated zwitterionic intermediate is strongly kinetically unfavorable, and external proton‐donor source is essential to complete quaternization. A molecular cluster of the intermediate with one molecule of water has been modeled for intermolecular reaction pathway, but even in this case, the proton transfer remains to be the rate‐determining step that is in a good agreement with previous kinetic investigations on this reaction. The data obtained for this reaction have much in common with recent studies on the mechanisms of the Morita–Baylis–Hillman reaction and phosphine‐catalyzed [3+2] cycloaddition, which revealed paramount importance of proton‐transfer steps. © 2013 Wiley Periodicals, Inc.

DFT Studies on Gold-Catalyzed Cycloisomerization of 1,5-Enynes

Gold-catalyzed cycloisomerization of 1,5-enynes has been investigated with the aid of density functional theory calculations at the B3LYP level of theory. We have examined how substituents influence the reaction paths in the cycloisomerization of 1,5-enynes catalyzed by both AuCl and [AuL]+ (L = phosphine).

Prediction of monomer reactivity parameters using quantum chemical descriptors

To construct artificial neural network (ANN) models for the prediction of reactivity parameters (u, ν), density functional theory (DFT) calculations are carried out for 55 vinyl monomers, at the B3LYP level of theory with a 6–31G(d) basis set. After the generation of quantum chemical descriptors, the stepwise multiple linear regression (MLR) analysis and the ANN method are used to develop quantitative structure-property relationship (QSPR) models of parameters u and ν. The ANN models produced test set root-mean-square (rms) errors of 0.35 for the parameter u and 0.34 for the parameter ν. Research results indicate that the QSPR models based on DFT calculations and ANN techniques are accurate and possess the ability to generalize.

Isolation of the Pyrrolizidine Alkaloid Intermedine-N-oxide from Cerinthe glabra and ab initio Calculation of its 13C NMR Shifts

The pyrrolizidine alkaloid intermedine-N-oxide was isolated from Cerinthe glabra for the first time. Due to the questionable assignments of NMR signals of this compound in previous literature reports ab initio calculations of the 13C NMR values based on the GIAO approach, using HF and B3LYP levels of theory and the four basis sets 6-31G(d), 6-311G(d), 6-31G(d,p), and 6-311G(d,p) were performed. The assignments obtained this way are in very good accordance with the experimental values.

A Density Functional Theory Study of Cyclization of Citronellal

A theoretical study of the kinetics and mechanism of the cyclization of citronellal in the gas phase was performed using density functional theory methods at the B3LYP level of theory with 6-311G, 6-311G*, 6-31G**, 6-311G**, 6-311+G and 6-311 + +G basis sets at 298.15K, 433.15K, and 473.15K. Equilibrium molecular geometries and harmonic vibrational frequencies of the reactant, transition state and products were calculated. Rate constants and activation thermodynamic parameters were calculated and showed a fairly good agreement with experimental results. The effect of solvent polarity on the reaction was studied. These calculations indicated that the reaction proceeds through an asynchronous concerted mechanism.

A detailed quantum chemical study of the interactions of [Pt(dien)Cl]+ with a series of S-donor ligands: A computational approach

The mechanism of substitution reaction of [Pt(dien)Cl]+ (dien=diethylenetriamine) with a series of endogenous and exogenous S-containing ligands such as H2S, sodium methanethiolate (NaSMe), dimethylsulfane (Me2S), diethylsulfane (Et2S), thiourea (TU), 1,3-dimethylthiourea (DMTU), 1,3-diethylthiourea (DMTU), sodium-2-mercaptoethanesulfonate (mesna), sodium diethyldithiocarbamate (Naddtc), l-methionine (Met) and l-cysteine (Cys) were studied by computational methods. Within the framework of transition state theory, DFT-based calculations were performed in gas phase using the B3LYP exchange–correlation functionals as implemented in the Gaussian 09 program. Pentacoordinated square pyramidal (SP) and trigonal–bipyramidal (TBP)-like structure transition states (TS) along with other stationary points on potential energy surface were optimized and characterized. Results led us to conclude that for platination of S-ligands as protecting agents Naddtc, mesna and TU are more suitable than thiol and thioether ligands. Natural bond orbital (NBO) analysis method was performed for the investigation of major stabilizing orbital interactions. To obtain accurate energies for the reaction surfaces, single-point energies were calculated by conductor-like polarisable calculation model (CPCM) using larger basis sets at MP2 and B3LYP levels of theory. The sequence of rate constants found in our study in aqueous phase is: Naddtc>mesna>TU>Met>Cys>Me2S>Et2S≈MeSH>H2S≈DETU>NaSMe>DMTU.

Dispersion energy enforced dimerization of a cyclic disilylated plumbylene.

By reaction of 1,4-dipotassio-1,1,4,4-tetrakis(trimethylsilyl)tetramethyltetrasilane with PbBr2 in the presence of triethylphosphine a base adduct of a cyclic disilylated plumbylene could be obtained. Phosphine abstraction with B(C6F5)3 led to formation of a base-free plumbylene dimer, which features an unexpected single donor–acceptor PbPb bond. The results of density functional computations at the M06-2X and B3LYP level of theory indicate that the dominating interactions which hold the plumbylene subunits together and which define its actual molecular structure are attracting van der Waals forces between the two large and polarizable plumbylene subunits.

A quantum chemical study on the thermal degradation reaction of polyesters

We carried out a theoretical study on the mechanism of the thermal degradation reaction of polyesters by using the B3LYP level of theory. β elimination reaction of ethylene-, propylene-1,3-, and butylene-1,4-dibenzoates are investigated as model systems for poly(ethylene terephthalate), poly(propylene terephthalate) and poly(butylene terephthalate), respectively. Catalysis mechanism of Sb(OEt)3, Ge(OEt)4, Ti(OEt)4 and Zn(OAc)2 is also investigated. Although the catalysis mechanism in β elimination reaction is generally thought to be electron-withdrawing effect of a Lewis acidity of metal center, the activation energies in this mechanism was calculated to be very similar to those in non-catalyzed reactions and no catalytic effect was observed. We found that β hydrogen abstraction by the alkoxy ligand of catalyst is more favorable reaction path; the activation energy for non-catalyzed thermal degradation reaction of ethylene dibenzoate in vacuo is 51.1 kcal/mol, whereas that in alkoxy ligand mechanism is 43.8 kcal/mol.

Isomeric identification of methylated naphthalenes using gas phase infrared spectroscopy

We report gas phase mid-infrared spectra of 1- and 2- methyl naphthalenes at 0.2 cm−1 resolution. Assignment of observed bands have been made using scaled quantum mechanical (SQM) calculations where the force fields rather the frequencies are scaled to find a close fit between observed and calculated bands. The structure of the molecules has been optimized using B3LYP level of theory in conjunction with standard 6-311G** basis set to obtain the harmonic frequencies. Using the force constants in Cartesian coordinates from the Gaussian output, scaled force field calculations are carried out using a modified version of the UMAT program in the QCPE package. Potential energy distributions of the normal modes obtained from such calculations helped us assign the observed bands and identify the unique features of the spectra of 1- and 2-MNs which are important for their isomeric identification.

DFTr Studies of Five‐ and Six‐Residue Cyclic‐β(1→4) Cellulosic Molecules

Density functional (DFT) conformational in vacuo studies of cellobiose have shown that ϕ(H) -anti conformations are low in energy relative to the syn forms, while the ψ(H) -anti forms are higher in energy. Further, as the cellulosic fragments became larger than a disaccharide and new hydrogen bonding interactions between multiple residues become available, stable low energy ϕ(H) -anti, and ψ(H) -anti cellulosic structures became possible. To test the stability of cyclic anti-conformations, a number of β-linked five- and six-residue molecules were created and then energy optimized in solvent (water, n-heptane) using the implicit solvation method COSMO at the B3LYP level of theory. The created symmetric cyclic structures were without distortion. Upon optimization some cyclic conformations were found to be of low energy when compared with linear five- and six-residue chains, after correcting the energy for the exclusion of a water molecule upon cyclization. It was also obvious from the hydrogen bonding network formed above and below the plane of the cyclic structure that these structures could exhibit strong synergistic tendencies. The conformational energy preferences for clockwise "c" and counter-clockwise "r" hydroxyl groups and preference for the hydroxymethyl rotamers is described. Because these structures contain energetically unfavorable flipped conformations in water, that is, dihedral angles of ∼180°/0° or ∼0°/180° in ϕ(H) /ψ(H) , it is clear that the synthesis of these compounds will be challenging.

Synthesis, 15N NMR spectra and GIAO calculated data of the seven positional isomers of 15N-labeled N,N-dimethylsulfamoylquinoline

Abstract The one-step synthesis of positional isomers of N , N -dimethylsulfamoylquinoline are presented. Seven newly synthesized compounds have been characterized by elemental analyses, MS, 1 H and 15 N NMR spectral data. The long-range correlations between the ring protons and the endocyclic nitrogen atoms were observed in the gHMBC experiments. The spectral positions of the nitrogen atoms from the sulfonamide groups were drawn from the 1D spectra of the 15 N-labeled sulfonamide isotopomers. Correlations between the experimentally determined chemical shifts and GIAO calculated isotropic shielding constants were found. The GIAO calculations were based on HF-, MP2-, and B3LYP-optimized geometries and were performed at the HF, BLYP, and B3LYP levels of theory.