B3LYP Level Of Theory Research Articles

Theoretical and experimental electrostatic potential around the m-nitrophenol molecule.

This work concerns a comparison of experimental and theoretical results of the electron charge density distribution and the electrostatic potential around the m-nitrophenol molecule (m-NPH) known for its interesting physical characteristics. The molecular experimental results have been obtained from a high-resolution X-ray diffraction study. Theoretical investigations were performed using the Density Functional Theory at B3LYP level of theory at 6-31G* in the Gaussian program. The multipolar model of Hansen and Coppens was used for the experimental electron charge density distribution around the molecule, while we used the DFT methods for the theoretical calculations. The electron charge density obtained in both methods allowed us to find out different molecular properties such us the electrostatic potential and the dipole moment, which were finally subject to a comparison leading to a good match obtained between both methods. The intramolecular charge transfer has also been confirmed by an HOMO-LUMO analysis.

Electron diffraction analysis for the molecules with multiple large-amplitude motions. 3-nitrostyrene--a molecule with two internal rotors.

Dynamic structural analysis of the molecules possessing large-amplitude degrees of freedom has been attempted by many researchers; however, so far, electron diffraction investigations involved only one large-amplitude coordinate (internal rotation or bending). The current state of computational facilities allows extending of the general dynamic approach to the systems possessing two or more large-amplitude motions. This paper presents the first practical implementation of the theoretical method developed previously by the authors for solving the dynamic-structural problem with two or more large-amplitude coordinates; the procedure is applied to a molecule of 3-nitrostyrene. The molecule is represented as a set of pseudoconformers built on a two-dimensional grid corresponding to both internal rotation coordinates present in the molecule (with 10-30° steps by each angle); altogether, up to 342 pseudoconformers were used. Structural analysis was based on the experimental electron diffraction data supported by quantum chemical calculations (at the MP2 and B3LYP levels of theory) and molecular spectroscopy data. Quantum chemistry predicts the planar structure of both syn- and anti- stable conformations with close energies and weak interaction between internal rotations of nitro and vinyl groups. The gas-phase electron diffraction experimental data are compatible with the quantum chemical predictions. The principal equilibrium geometry parameters of the molecule (syn- conformation) have been determined as follows: r(e)(C-C)(ring, avg.) = 1.391(1) Å, r(e)(C-C) = 1.477(5) Å, r(e)(C═C) = 1.333(7) Å, r(e)(C-N) = 1.463(5) Å, r(e)(N═O) = 1.227(3) Å, ∠e(O═N═O) = 124.3 (4)°. Experimental data for this molecule are insufficient to make estimates of the barrier heights of internal rotation; the population ratio of syn- and anti- conformations is evaluated as 50 ± 20%. Results of our investigation confirm the presence of significant internal rotations in the 3-nitrostyrene molecule.

ChemInform Abstract: Fluoro‐Ene Reaction versus [2 + 2] Cycloaddition in the Thermal C2—C6 Cyclization of Enyne‐Allenes: An Experimental and Theoretical Investigation.

A series of fluoroalkyl-substituted enyne-allenes have been synthesized by a new route with the aim of elucidating the possibility of a fluoro-ene reaction via an intermediate fulvenyl diradical generated in the thermal C2–C6 (Schmittel) cyclization reaction. As a result of the strong C–F bond, fluorine atom transfer was not observed. Instead, 1H-cyclobuta[a]indenes were formed in good yields despite the high strain energy. DFT calculations at the B3LYP level of theory indicated that although the fluoro-ene reaction is the most exothermic reaction available, cyclobutene formation is kinetically favored over the [1,5]-fluorine shift by 5–15 kcal mol–1 in various model compounds.

Mono and digallium selenide clusters as potential superhalogens.

We present a systematic theoretical study on mono and digallium selenide clusters, Ga(m)Se(n) (m = 1, 2 and n = 1-4), along with their negatively and positively charged counterparts. Different theoretical methods, namely density functional theory (DFT), second-order Møller-Plesset perturbation theory (MP2) and coupled cluster singles and doubles, including non-iterative triples [CCSD(T)], were employed in conjunction with the 6-311+G(2df) basis set. The lowest-energy configurations of gallium selenides prefer to be planar, with the exception of cationic GaSe4 and Ga2Se4. The adiabatic electron affinities (AEA) of Ga(m)Se(n) (m = 1, 2 and n = 1-4) clusters range from 1.07 to 3.78 eV, and their adiabatic ionization potentials (AIP) vary from 7.57 to 8.76 eV using the CCSD(T)//B3LYP level of theory. It was found that the AEAs of gallium selenides do not depend solely on the electrophilicity of the clusters but also on their electronic structures. No significant trend was observed in the AIP values and HOMO-LUMO (H-L) gaps with increase in cluster size of the mono and digallium selenide series. Among the dissociation channels, the decomposition of GaSe4 → GaSe2 + Se2 was found to be thermodynamically most favored. Furthermore, the AEAs of GaSe2, GaSe3, GaSe4 and Ga2Se4 were found to exceed that of the chlorine atom and are therefore termed as 'superhalogens'. Finally, the AEAs of the Ga2X(n) (X = O-Se; n = 2-4) series were found to be almost similar.

DFT and Vibrational Spectroscopic Study on 3-alkyl-4-amino-6-aryl-1, 2, 4-triazin-5-one Herbicide

Density functional theory and vibrational analysis of 3-alkyl-4-amino-6-aryl-1,2,4-triazin-5-one herbicide has been carried out. The geometry has been optimized by B3LYP level of theories using 6-311G (df, p) basis set using Gaussian 09 program and compared with the crystal data. NBO and structural analysis has been carried out on the compound. Theoretical methods have been used to study the proper and improper hydrogen bonds, considering the hydrogen bond length and charge transfer. The Mulliken population analysis on atomic charges and the HOMO-LUMO energy were also calculated.

Katoite under pressure: an ab initio investigation of its structural, elastic and vibrational properties sheds light on the phase transition.

The evolution under pressures up to 65 GPa of structural, elastic and vibrational properties of the katoite hydrogarnet, Ca3Al2(OH)12, is investigated with an ab initio simulation performed at the B3LYP level of theory, by using all-electron basis sets with the Crystal periodic program. The high-symmetry Ia3d phase of katoite, stable under ambient conditions, is shown to be destabilized, as pressure increases, by interactions involving hydrogen atoms and their neighbors which weaken the hydrogen bonding network of the structure. The corresponding thermodynamical instability is revealed by anomalous deviations from regularity of its elastic constants and by numerous imaginary phonon frequencies, up to 50 GPa. Interestingly, as pressure is further increased above 50 GPa, the Ia3d structure is shown to become stable again (all positive phonon frequencies and regular elastic constants). However, present calculations suggest that, above about 15 GPa and up to at least 65 GPa, a phase of I4[combining macron]3d symmetry (a non-centrosymmetric subgroup of Ia3d) becomes more stable than the Ia3d one, being characterized by strengthened hydrogen bonds. At low-pressures (between about 5 GPa and 15 GPa), both phases show some instabilities (more so for I4[combining macron]3d than for Ia3d), thus suggesting either the existence of a third phase or a possible phase transition of second order.

Computational Investigations about the Ground and Excited States’Properties of Trans-4-N,N-Dimethylamino-4’-Nitro-Stilbene (DNS) and Trans-4-N,N-Dimethyl-Amino-4’-Cyanostilbene (DCS) Derivatives

The ground and lowest-lying singlet excited state geometries and dipole moments of trans-4-N,N-dimethylamino- 4’-nitro-stilbene (DNS) derivative and the trans-4-N,N-dimethyl-amino-4’-cyanostilbene (DCS) derivative are calculated at the B3LYP level of theory for the first time in this work. The vertical excitation energies and the fluorescence emission energies are obtained for the two species. The calculated results are compared with available experimental results and show good consistency. The molecular orbital analyses in these molecules have been performed. The comparison of the atomic charge distributions in the ground and excited states of both the DNS derivative and DCS derivative implies the intra molecular charge transfer (ICT) process during the excitation period.

Interaction between transition metals and phenylalanine: A combined experimental and computational study

Some transition metal complexes of phenylalanine of general formula [M(C9H10NO2)2]; where M=Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) are prepared in aqueous medium and characterized by spectroscopic, thermo-gravimetric (TG) and magnetic susceptibility analysis. Density functional theory (DFT) has been employed calculating the equilibrium geometries and vibrational frequencies of those complexes at B3LYP level of theory using 6-31G(d) and SDD basis sets. In addition, frontier molecular orbital and time-dependent density functional theory (TD-DFT) calculations are performed with CAM-B3LYP/6-31+G(d,p) and B3LYP/SDD level of theories. Thermo-gravimetric analysis confirms the composition of the complexes by comparing the experimental and calculated data for C, H, N and metals. Experimental and computed IR results predict a significant change in vibrational frequencies of metal-phenylalanine complexes compared to free ligand. DFT calculation confirms that Mn, Co, Ni and Cu complexes form square planar structure whereas Zn adopts distorted tetrahedral geometry. The metal–oxygen bonds in the optimized geometry of all complexes are shorter compared to the metal–nitrogen bonds which is consistent with a previous study. Cation-binding energy, enthalpy and Gibbs free energy indicates that these complexes are thermodynamically stable. UV–vis and TD-DFT studies reveal that these complexes demonstrate representative metal-to-ligand charge transfer (MLCT) and d–d transitions bands. TG analysis and IR spectra of the metal complexes strongly support the absence of water in crystallization. Magnetic susceptibility data of the complexes exhibits that all except Zn(II) complex are high spin paramagnetic.

DFT study on foscarnet as an antiviral drug: Conformer analysis, gas phase acidity, metal ion affinity and influence of metal complexation on gas phase acidity

This work presents a density functional theory study of Foscarnet (FOS), an anti-viral drug. In this study conformational analysis, gas phase acidity and metal ion affinity (MIA) of foscarnet with selected cations from alkalis (Li+, Na+, and K+) and alkaline earths (Ca2+ and Mg2+) were calculated. All of the structure optimizations and frequency calculations were performed at the B3LYP level of theory with 6-311++G(d,p) basis set. The calculations showed the MIA order to be K+<Na+<Li+<Ca2+<Mg2+, in agreement with increasing gas phase acidity of the foscarnet molecule during complexation. Natural bond orbital theory (NBO) and quantum theory of atoms in molecules (QTAIM) were used to investigate the charge transfer process and the nature of interactions in the formed complexes. The results of the NBO analysis revealed that Mn+ acts as charge acceptor and the amount of charge transfer is in agreement with MIA. The QTAIM analysis shows that (MO) coordinations are electrostatic in nature, and their strengths are in agreement with electron densities at their bond critical points (BCP).

Kinetics, mechanism and thermodynamics of reactions of CH3NHNH2 with OOH

Reactions between CH3NHNH2 and OOH radical were studied using computational methods. The activation energies (Ea) and Gibbs free energies of activation (ΔG#) were calculated at the MP2 and B3LYP levels of theory. The calculated activation energies of the hydrogen abstraction reactions were less than 100 kJ/mol and those for the substitution reactions were about 150–250 kJ/mol. The calculated activation energies for the intra-molecular hydrogen transfer reactions in CH3NHNH, CH2NNH2 and CH3NN molecules were 210–250 kJ/mol. Catalytic effect of the water molecule on the intra-molecular hydrogen transfer reactions was studied. It was found that the water molecule decreases the activation energies by about 70–100 kJ/mol. Rate constants of the reactions were calculated using transition state theory in the temperature range of 298–2000 K. Consecutive hydrogen abstraction reactions from CH3NHNH2 led to the formation of CH2NN, which was a very stable molecule.

A DFT Study of 1,3-dipolar Cycloaddition Reaction of Benzonitrile Oxide and N-aryl-2,4,6-heptatrien-1-imine

A theoretical study of the effect of substitution on the 1,3-dipolar cycloaddition of benzonitrile oxide was performed using the DFT method at the B3LYP level of theory using 6–311G(d,p) basis sets. Equilibrium molecular geometries and harmonic vibrational frequencies of the reactants, transition state, and product were calculated. The corresponding rate constants and activation parameters were calculated. The results showed good agreement with experimental data. These calculations indicated that the reaction proceeds through an asynchronous mechanism.

Theoretical Study on the Extraction of Alkaline Earth Salts by 18-Crown-6: Roles of Counterions, Solvent Types and Extraction Temperatures

The roles of counterions, solvent types and extraction temperatures on the selectivity of 18-crown-6 (L) toward alkaline earth salts MX2 (M = Ca, Sr, Ba; X = Cl-, NO3-) have been studied by density functional method at B3LYP level of theory in gas and solvent phase. In gas phase, the chloride anion Cl- is the preference counterion than nitrate anion NO3-. This result is confirmed by the interaction energies, the second order interaction energies, charge transfers, energy difference between HOMO-LUMO and electrostatic potential maps. The presence of solvent reversed the gas phase trend. It is found that NO3- is the preference counterion in solvent phase. The calculated free energies demonstrate that the solvent types strongly change the strength of the complex formation. The free energies are exothermic in polar solvent while for the non polar solvent the free energies are endothermic. As the temperature changes the free energies also vary where the higher the temperatures the lower the free energy values. The calculated free energies are correlated well with the experimental stability constants. This theoretical study would have a strong contribution in planning the experimental conditions in terms of the preference counterions, solvent types and optimum extraction temperatures.

Synthesis, Crystal Structure and Characterization of Cu(II) and Cd(II) Coordination Compounds Based on Ligand 2-(3-(Pyridin-2-yl)-1H-pyrazol-1-yl)acetic Acid

Two novel coordination compounds [Cu2(pypya)3(H2O)2]·Cl·(H2O)5 (1) and {[Cd(pypya)(ta)1/2]·H2O}n (2) (Hpypya=2-(3-(pyridin-2-yl)-1H-pyrazol-1-yl)acetic acid, H2ta=terephthalic acid) were synthesized and characterized by single X-ray diffraction. Structure determination reveals that complex 1 and complex 2 crystallize in the triclinic system, with the P-1 space group. The asymmetric unit of 1 contains two Cu(II) ions, and their coordination modes are different. These units of complex 1 are linked together via hydrogen bonds and π-π interactions, and the 3D structure of complex 1 was formed. Complex 2, a mononuclear Cd(II) coordination compound, has a 2D structure which was constructed via coordination bonds. TGA and fluorescence spectra analysis of complex 1 and complex 2 have also been studied. In addition, the geometry parameters of complex 1 have been optimized with the B3LYP method of density functional theory (DFT) to explain its coordination behavior. The electronic properties of the complex 1 and ligand Hpypya have been investigated based on the nature bond orbital (NBO) analysis at the B3LYP level of theory. The result verifies that the synergistic effect have occurred in the compound.

Crystal structure of a new monoclinic polymorph of N-(4-methyl-phen-yl)-3-nitro-pyridin-2-amine.

The title compound, C12H11N3O2, is a second monoclinic polymorph (P21, with Z' = 4) of the previously reported monoclinic (P21/c, with Z' = 2) form [Akhmad Aznan et al. (2010 ▶). Acta Cryst. E66, o2400]. Four independent mol-ecules comprise the asymmetric unit, which have the common features of a syn disposition of the pyridine N atom and the toluene ring, and an intra-molecular amine-nitro N-H⋯O hydrogen bond. The differences between mol-ecules relate to the dihedral angles between the rings which range from 2.92 (19) to 26.24 (19)°. The geometry-optimized structure [B3LYP level of theory and 6-311 g+(d,p) basis set] has the same features except that the entire mol-ecule is planar. In the crystal, the three-dimensional architecture is consolidated by a combination of C-H⋯O, C-H⋯π, nitro-N-O⋯π and π-π inter-actions [inter-centroid distances = 3.649 (2)-3.916 (2) Å].

Fluoro‐Ene Reaction Versus [2+2] Cycloaddition in the Thermal C2–C6 Cyclization of Enyne‐Allenes: An Experimental and Theoretical Investigation

AbstractA series of fluoroalkyl‐substituted enyne‐allenes have been synthesized by a new route with the aim of elucidating the possibility of a fluoro‐ene reaction via an intermediate fulvenyl diradical generated in the thermal C2–C6 (Schmittel) cyclization reaction. As a result of the strong C–F bond, fluorine atom transfer was not observed. Instead, 1H‐cyclobuta[a]indenes were formed in good yields despite the high strain energy. DFT calculations at the B3LYP level of theory indicated that although the fluoro‐ene reaction is the most exothermic reaction available, cyclobutene formation is kinetically favored over the [1,5]‐fluorine shift by 5–15 kcal mol–1 in various model compounds.

Computational study of exchange coupling in homo- and heterometallic oxo- and carboxylato bridged trinuclear complexes with triangular {FeIII2M(μ3-O)} (M = FeIII, NiII, CoII) core

Using broken symmetry approach (DFT-BS, 6-311G(d)/B3LYP level of theory) the structure and magnetic exchange interactions in homo- and heterometallic oxo-centered trinuclear carboxylate complexes [Fe2M(μ3-O)(RCO2)6(H2O)3]n+ (M=FeIII, n=1; NiII, CoII, n=0; R=C(CH3)3, CH3, CCl3, CF3) were evaluated. The influence of metal ion and the nature of the carboxylate bridging ligand on the structure and magnetic properties of trinuclear complex is discussed. It was shown, that antiferromagnetic exchange interactions in both FeIII–FeIII and FeIII–MII (M=Ni, Co) pairs weakens in the row trimethylacetate>acetate>trichloroacetate≈trifluoroacetate.

A study of the experimental and theoretical infrared, Raman, 1H and 13C NMR spectra of the biochemicals valeric and valproic acids

The structural stability, vibrational, 1H and 13C NMR spectra of valeric and valproic acids were investigated by the B3LYP calculations with the 6-311G** basis set. Valeric acid is predicted to exist predominantly in the planar cis form (80% abundance). Valproic acid is predicted to have an equilibrium mixture of 68% gauche-1 and 32% gauche-2 structures at 298.15K. The spectral feature of the OH stretching mode in the infrared spectra of both acids suggests the presence of strong H-bonding in the condensed phase of valeric acid and weak H-bonding in the case of valproic acid. The harmonic and anharmonic vibrational wavenumbers were computed at the B3LYP level of theory and tentative vibrational assignments were provided on the basis of combined theoretical and experimental infrared and Raman data of the molecules. Not all of the calculated anharmonic wavenumbers showed a consistent trend with the observed wavenumbers. The 1H and 13C NMR spectra of both acids were interpreted by experimental and DFT calculated chemical shifts of the two acids. The RMSD between experimental and theoretical 1H and 13C chemical shifts for valeric acid is 1.8 and 3.8ppm, whereas for valproic acid, it is 1.4 and 4.5ppm, respectively.

Disiline-doped boron nitride nanotubes: A computational study

The properties of the electronic structure of the Disiline-doped boron nitride nanotubes (Disiline-BNNTs) are investigated by a density functional theory (DFT) calculation. The structural forms are firstly optimized and the CS tensors calculated. Subsequently, the chemical-shielding isotropic (CSI) and chemical shielding anisotropic (CSA) parameters are found. The shielding values of boron (B) and nitrogen (N) atoms were calculated by Gauge-Including Atomic Orbital (GIAO), Continuous Set of Gauge Transformations (CSGT) and Individual Gauges for Atoms in Molecules (IGAIM) methods, using B3LYP/6-311+G*. The B3LYP level of theory with IGAIM was the best method to evaluate the theoretical chemical shifts for studied models. The results reveal a significant effect of Disiline doping on the chemical shielding tensors at the sites of those 11B and 15N nuclei located in the nearest neighborhood of the Disiline-doped ring. Furthermore, the values of dipole moments and HOMO-LUMO gaps change in the Disiline-doped models in comparison with the original pristine model.

Ab initio calculations of 13C NMR chemical shielding in some N4O2, N4S2 and N6 Schiff base ligands containing piperazine moiety

The calculation of 13 C isotropic shielding constants by means of GIAO and CSGT methods of eight Schiff base ligands containing piperazine moiety at the Hartree-Fock and B3LYP levels of theory are presented. Good linear correlations between the calculated chemical shielding at gas-phase and experimental shift values in CDCl 3 solution were obtained. Density functional theory (DFT) calculations at the B3LYP/6-31G(2d,p) level of theory is used to optimize the geometry of ligands. Calculated nuclear magnetic resonance (NMR) chemical shifts 13 C are reported for the some N 4 O 2 , N 4 S 2 and N 6 Schiff base ligands containing piperazine moiety. In order to establish a convenient and consistent protocol to be employed for confirming the experimental 13 C NMR spectra of Schiff base ligands, different combinations of models and basis sets were considered. The most reliable results were obtained at B3LYP/6-311G++ (d,p) level and CSGT method which can be used to predict 13 C NMR chemical shifts with a very high accuracy for latter compounds. These results show the agreement between theoretical and experimental 13 C NMR chemical shielding of mentioned ligands.

Quantum localization/delocalization of muonium in the glycine–K+ complex

Previous electronic structure studies have revealed that the glycine–K+ complex has a low-barrier intramolecular proton-transfer pathway between zwitterionic and neutral forms. We have theoretically calculated quantum molecular structures of this complex including the proton-transfer process using a path-integral molecular dynamics technique on an interpolated potential energy surface developed at the B3LYP level of theory. When the transferring proton is substituted by muon, it was found that the muonium atom showed a broad distribution around the proton(muon)-transfer transition state region between the neutral and zwitterionic structures due to extreme nuclear quantum effects of a very light particle although the distribution peak is slightly deviated from the transition state. The present study demonstrates that Mu can be employed to probe transition-state regions of potential energy surfaces of proton-transfer chemical reactions.