Showing papers in "Journal of Molecular Structure-theochem in 2007"
TL;DR: In this article, the polynomial solution of the Schrodinger equation for the Pseudoharmonic potential is found for any arbitrary angular momentum l. The exact bound-state energy eigenvalues and the corresponding eigenfunctions are analytically calculated.
Abstract: The polynomial solution of the Schrodinger equation for the Pseudoharmonic potential is found for any arbitrary angular momentum l. The exact bound-state energy eigenvalues and the corresponding eigenfunctions are analytically calculated. The energy states for several diatomic molecular systems are calculated numerically for various principal and angular quantum numbers. By a proper transformation, this problem is also solved very simply by using the known eigensolutions of anharmonic oscillator potential.
154 citations
TL;DR: In this article, the reactivities of the intrinsic and aluminum-doped single-walled (8, 0) carbon nanotube (SWCNT) with CO using density functional theory (DFT) calculations were investigated.
Abstract: In order to explore a novel sensor to detect the gaseous molecules, we investigate reactivities of the intrinsic and aluminum-doped (Al-doped) single-walled (8, 0) carbon nanotube (SWCNT) with CO using density functional theory (DFT) calculations. The Al-doped SWCNT presents high sensitivity to CO, compared with the intrinsic SWCNT, as indicated by the calculated geometrical structures and electronic properties for these systems. Al-doped SWCNTs are expected to be a potential candidate for detecting the presence of CO.
128 citations
TL;DR: Through space NMR shieldings of aromatic (benzene, mono-substituted and annelated benzenes, ferrocene, [14]- and [18]-annulenes, phenylenes and tetra-to-heptahelicene) and anti-aromatic molecules (cyclobutadiene and pentalene) were assessed by ab initio molecular-orbital calculations.
Abstract: Through space NMR shieldings of aromatic (benzene, mono-substituted and annelated benzenes, ferrocene, [14]- and [18]-annulenes, phenylenes and tetra- to heptahelicene) and anti-aromatic molecules (cyclobutadiene and pentalene) were assessed by ab initio molecular-orbital calculations. Employing the nucleus-independent chemical shifts (NICS) concept, these through space NMR shieldings were visualized as iso-chemical-shielding surfaces (ICSSs) and can be applied quantitatively to determine the stereochemistry of proximal nuclei. In addition, the distances in A at ICSS values of ±0.1 ppm in-plane and perpendicular-to-center of the aromatic ring system were employed as a simple means to compare and estimate qualitatively the aromaticity of the systems at hand.
120 citations
TL;DR: In this paper, the nature of C-H⋯M agostic interactions in model metal complexes was studied with the natural bond orbital analysis (NBO) approach using density functional theory (DFT) optimized geometries at the B3LYP/6-31G(d,p) level of theory.
Abstract: The nature of C–H⋯M agostic interactions in model metal complexes [M2+(CH2CH3)(PH3)nCl] (where M = Sc, Ti, V, Ti, Cr, Mn, Fe, Co, Ni, Cu, Zn; n = 1, 2, 3, 4) was studied with the natural bond orbital analysis (NBO) approach using density functional theory (DFT) optimized geometries at the B3LYP/6-31G(d,p) level of theory. The effect of nature of metal, coordination number, oxidation state and ligand field effects on the agostic interaction is examined. A set of 20 crystal structures of organometallic complexes taken from the Cambridge Structural Database (CSD) was studied computationally employing AIM theory and NBO analysis, and the applicability of these methods was critically accessed in demarcating the two types of interaction.
79 citations
TL;DR: In this paper, a segmented contracted double zeta basis set of triple and quadruple zeta valence quality plus polarization functions for the atoms from H to Ar were reported, with the objective of having a better description of electron affinities, polarizabilities, and hydrogen bonding.
Abstract: Recently, segmented contracted basis sets of triple and quadruple zeta valence quality plus polarization functions for the atoms from H to Ar were reported. In this work, with the objective of having a better description of electron affinities, polarizabilities, and hydrogen bonding, each of these sets was augmented with diffuse (s and p symmetries) and polarization (p, d, f, and g symmetries) functions that were optimized for the anion at the Hartree–Fock (HF) and M ϕ ller–Plesset second-order (MP2) levels, respectively. This extends earlier work on segmented contracted double zeta valence basis set. In order to assess the quality of these sets, HF, MP2, and density functional theory calculations of electric dipole moment and static dipole polarizability and hyperpolarizability for a sample of molecules were carried out. The results are compared with theoretical and experimental values reported in the literature.
78 citations
TL;DR: In this article, a model based on a quantitative structure-property relationship (QSPR) was developed using multiple linear regression approach and quantum chemical descriptors derived from AM1-based calculations (MOPAC7.0) for determination of the acidity constants of some aromatic acid derivatives.
Abstract: A very simple, strong, descriptive and interpretable model, based on a quantitative structure–property relationship (QSPR), is developed using multiple linear regression approach and quantum chemical descriptors derived from AM1-based calculations (MOPAC7.0) for determination of the acidity constants of some aromatic acid derivatives. By molecular modeling and calculation of descriptors, three significant descriptors related to the pKa values of the acids, were identified. These are related to the partial charges at each atom in Oδ−–Hδ+ bond (pchgHδ+ and pchgOδ− −) and the changing of bond length in O–H molecular structures. A multiple linear regression (MLR) model based on 74 molecules as a training set has been developed for the prediction of the acidity constants of some aromatic acids using these quantum chemical descriptors. The effects of these theoretical descriptors on the acidity constants are discussed. The pKa values of aromatic acids generally decreased with increasing positive partial charges of acidic hydrogen atom. A model with low prediction error and high correlation coefficient was obtained. This model was used for the prediction of the pKa values of some aromatic acids (33 test acids) which were not used in the modeling procedure. The model obtained demonstrates excellent fit statistics and gives accurate predictions. The average relative error ( RE ¯ % ) of prediction set is lower than 1% and square correlation coefficient (R2) is 0.9882.
77 citations
TL;DR: In this paper, the influence of water on the cysteine conformation was estimated using the IEF-PCM/B3LYP/aug-cc-pVDZ calculations.
Abstract: Based on the B3LYP and MP2/aug-cc-pVDZ calculations, 51 cysteine conformers were found to be stable in the gas phase. The calculations were repeated for the most stable eight structures by using the aug-cc-pVTZ basis set. To estimate the influence of water on the cysteine conformation, the IEF-PCM/B3LYP/aug-cc-pVDZ calculations were carried out and showed 44 neutral and 12 zwitterion conformers to be stable in the water solution. The most stable cysteine structure in water appeared to be the zwitterionic conformer quite similar to the molecule observed in the crystal state.
71 citations
TL;DR: In this paper, a Monte Carlo simulation was used to investigate molecular association in pure liquid ethylene carbonate (EC) and propylene carbonates (PC), and the results of simulations with the partial charges set to zero revealed that the electrostatic term plays a determining role in structuring the liquids.
Abstract: Monte Carlo simulations have been used to investigate molecular association in pure liquid ethylene carbonate (EC) and propylene carbonate (PC). Standard force fields have been developed in order to reproduce accurately experimental pure liquid properties. Intermolecular interactions were described by combining standard OPLS Lennard–Jones parameters and partial atomic charges from fitting to the MP2/6-31G* electrostatic potential surface (EPS) with the CHELPG procedure. It was found that the inclusion of MP2 electron correlation on calculations of the partial atomic charges is required in order to achieve a proper description of the experimental liquid properties. The resultant force fields yielded average errors of 1–2% in computed densities and heats of vaporization. A thorough characterization of the liquid structures was performed with radial distribution functions, coordination numbers, energy distributions and dipole–dipole correlations. The electrostatic interactions in condensed phase lead the neighboring molecules to a preferential head to tail alignment of the dipoles. In contrast, the most energetically favored configuration for the EC and PC dimers in the gas phase exhibited antiparallel dipoles. The results of simulations with the partial charges set to zero revealed that the electrostatic term plays a determining role in structuring the liquids. Basis set dependence of EPS was investigated comparing the CHELPG MP2/6-31G* charges and dipole moments with the ones obtained at the MP2/{6-311G**, 6-31++G**, 6-311++G** and 6-311++G(3df,3pd)} level. Polarization effects due to intermolecular interaction were also investigate and a good reproduction of the experimental density and heat of vaporization (1.5% and 2% of deviation, respectively) was accomplished for liquid EC using CHELPG charges obtained for the most stable EC dimer configuration (antiparallel) at the MP2/6-31++G** level of theory.
64 citations
TL;DR: In this article, a 5 npT molecular dynamic simulation at T = 300 K and p = 1.0 ǫ atm was performed to investigate thermodynamical and structural properties of ionic liquid 1-butyl-3methylimidazolium tetrafluoroborate.
Abstract: Room-temperature ionic liquids (RTILs) due to their unique properties and solvent capabilities have been motivating an extraordinary growth on experimental and theoretical investigations. Many RTILs have been developed to fulfill specific applications and therefore this class of compounds has been termed “designer solvents”. Therefore, to accomplish this purpose, the understanding of RTILs behavior at the atomistic level is needed. In this work a 5 ns NpT molecular dynamic simulation at T = 300 K and p = 1.0 atm was performed to investigate thermodynamical and structural properties of ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate. All force field parameters but charges and geometries were taken from the OPLS-AA. The partial charges and geometry parameters were obtained at the ab initio MP2/6-31g(d) level, with charges computed using the ChelpG procedure. This same level of theory was used to calculate energies for cation–anion interactions at several configurations to validate the force field parameters. The agreement between geometries and energies obtained with ab initio and force field calculations is good. The value obtained for the liquid density, 1.178 g cm −3 , is close to the experimental data (1.17 g cm −3 ). The value estimated for the heat of vaporization, Δ H vap ≈ 413 kJ mol −1 , is larger than the ones usually observed for molecular liquids, which is in accordance with the very low vapor pressure observed for RTILs. Structural and dynamics properties, such as radial distribution function and mean square displacement were analyzed and are also in good agreement with data reported in the literature. Comparatively to the anion, the cation self-diffusion constant is larger despite the fact that it is heavier and bigger. Compared to the values observed for molecular liquids the self-diffusion constants obtained for cation and anions are about three orders of magnitude smaller.
61 citations
TL;DR: In this paper, the authors show that DBOCs to the total atomization energy are systematically overestimated at the SCF level, and that the correlation correction converges very rapidly with the basis set.
Abstract: A benchmark calculation of the atomization energy of the ‘simple’ organic molecule C 2 H 6 (ethane) has been carried out by means of W4 theory. While the molecule is straightforward in terms of one-particle and n -particle basis set convergence, its large zero-point vibrational energy (and anharmonic correction thereto) and nontrivial diagonal Born–Oppenheimer correction (DBOC) represent interesting challenges. For the W4 set of molecules and C 2 H 6 , we show that DBOCs to the total atomization energy are systematically overestimated at the SCF level, and that the correlation correction converges very rapidly with the basis set. Thus, even at the CISD/cc-pVDZ level, useful correlation corrections to the DBOC are obtained. When applying such a correction, overall agreement with experiment was only marginally improved, but a more significant improvement is seen when hydrogen-containing systems are considered in isolation. We conclude that for closed-shell organic molecules, the greatest obstacles to highly accurate computational thermochemistry may not lie in the solution of the clamped-nuclei Schrodinger equation, but rather in the zero-point vibrational energy and the diagonal Born–Oppenheimer correction.
60 citations
TL;DR: In this paper, a new approximation formalism is applied to study the bound states of the Hellmann potential, which represents the superposition of the attractive Coulomb potential − a / r and the Yukawa potential b ǫexp(− δr )/ r of arbitrary strength b and screening parameter δ.
Abstract: A new approximation formalism is applied to study the bound states of the Hellmann potential, which represents the superposition of the attractive Coulomb potential − a / r and the Yukawa potential b exp (− δr )/ r of arbitrary strength b and screening parameter δ . Although the analytic expressions for the energy eigenvalues E n ,l yield quite accurate results for a wide range of n , l in the limit of very weak screening, the results become gradually worse as the strength b and the screening coefficient δ increase. This is because that the expansion parameter is not sufficiently small enough to guarantee the convergence of the expansion series for the energy levels.
TL;DR: In this article, a generalized Romberg differentiation procedure for numerical evaluation of first-order and higher-order derivatives is proposed, which is more robust in treating rounding errors, as shown by numerical tests.
Abstract: A generalized Romberg differentiation procedure decreasing truncation errors for numerical evaluation of first-order as well as higher-order derivatives is proposed. In comparison with the original Romberg method the higher-order terms are eliminated more efficiently. Moreover, the generalized scheme is more robust in treating rounding errors, as shown by numerical tests. The proposed method can find a wide range of applications including the evaluation of electronic and vibrational (hyper)polarizabilities.
TL;DR: In this paper, electron density analysis within the framework of Quantum Theory of Atoms in Molecules (QTAIM) indicates bond paths between oxygen atoms in open conformers of enol forms of cis -β-diketones.
Abstract: Electron density analysis within the framework of Quantum Theory of Atoms in Molecules (QTAIM) indicates bond paths between oxygen atoms in open conformers of enol forms of cis -β-diketones. The calculation of atomic energies shows that such a O O interaction in 1,8-naphthalenediol rather than denoting the presence of “non-bonded steric repulsion” can impart as much as 11 kcal/mol (in B3LYP) and 16 kcal/mol (in MP2) of local stabilization to the total energy of the molecule. In addition, QTAIM is also used to characterize these O O interactions. In the studied cases, QTAIM parameters at the BCP of O O bond, including electron density, the Laplacian of the electron density, the energy density and the ellipticity, exhibit the characteristics of closed shell interactions. Delocalization indices between oxygen atoms indicate very little sharing between oxygen atomic basins, which can be interpreted as small O O bond orders.
TL;DR: In this paper, the ONIOM-G3B3 method was used to predict the bond dissociation enthalpies (BDEs) of coenzyme Q, flavonoids, olives, curcumins, indolinonic hydroxylamines, phenothiazines, edaravones and antioxidants used as food additives.
Abstract: Radical-scavenging antioxidants play vital roles in the prevention of oxidative damage caused by free radicals, which is involved in many important chemical and biological processes. Using the ONIOM-G3B3 method, the bond dissociation enthalpies (BDEs) of coenzyme Q, flavonoids, olives, curcumins, indolinonic hydroxylamines, phenothiazines, edaravones and antioxidants used as food additives are predicted in the present study. On the basis of the computed BDE values, discussions were then made about their antioxidant activities, structure–activity relationships, and radical scavenging mechanisms. This work may be useful to clarify the radical scavenging mechanism of antioxidants and to design novel antioxidants.
TL;DR: In this article, the structure and electronic properties of armchair boron nitride nanotubes have been investigated as a function of tube diameter using density functional theory, where the length of each nanotube is kept constant.
Abstract: The structure and electronic properties of armchair boron nitride nanotubes have been investigated as a function of tube diameter using density functional theory. The length of each nanotube is kept constant. The structural parameters of the open end nanotube are studied. The variation in structural parameters is analyzed based on atomic charges of Mulliken and natural population analyses schemes. A topological analysis for charge density (ρ), and its second derivative (∇2ρ) for bonds have been performed using atoms in molecules (AIM) theory. Finally, the analysis of the charge distribution and charge transfer processes have been studied using the NBO partitioning scheme, which helps us to understand the interactions inside the boron nitride nanotubes which are responsible for the stabilization of the armchair boron nitride nanotubes.
TL;DR: In this article, the influence of the intramolecular hydrogen bond engaging the oxygen atom of the carbonyl group characterising acylated phloroglucinols, and of the geometrical features of the PHG skeleton, is investigated on four model structures, selected in such a way as to cover all the aspects of interest.
Abstract: Acylated phloroglucinols are widely spread in nature. Many of them exhibit biological activities, and the natural materials in which they are found have been used in traditional medicine. However, theoretical studies on phloroglucinols are rare, and they have mostly concerned the parent compound, 1,3,5-trihydroxybenzene. In the current work, the influence, on conformational preferences and energy, of the intramolecular hydrogen bond engaging the oxygen atom of the carbonyl group characterising acylated phloroglucinols, and of the geometrical features of the phloroglucinol skeleton, is investigated on four model structures, selected in such a way as to cover all the aspects of interest. All the possible geometrical options for each of these structures were calculated and compared. The results show a preference for the H-bond to form on the same side of a second substituent chain (when present) and the influence of the various aspects of the orientation of the OH groups. These results can constitute a reference for the study of acylated phloroglucinols in general and, more specifically, of acylated phloroglucinols having a second substituent chain besides the acyl chain, as confirmed by the study of the caespitate molecule, an acylated and prenylated phloroglucinol whose prenyl chain ends with an acetic-acid ester group. The presence of the ester function enables the formation of a second intramolecular H-bond with a variety of different geometries for the resulting ring, and conformers with both intramolecular H-bonds account for practically the total population. All the calculations were performed at HF level with the 6-31-G(d,p) basis set. The performance of AM1 and PM3 semiempirical methods was also investigated and found not completely adequate.
TL;DR: In this article, an extension of a quantum non-adiabatic treatment of H-bonds is presented, in which effects of anharmonicities of the high frequency XH→⋯Y and the low frequency X←H→Y→ modes on the υX-H infrared lineshapes of Hbonds systems are considered.
Abstract: The paper presents extension of a quantum non-adiabatic treatment of H-bonds in which effects of anharmonicities of the high frequency XH→⋯Y and the low frequency X←H⋯Y→ modes on the υX–H infrared lineshapes of H-bonds systems are considered. The anharmonic coupling between the high frequency XH→⋯Y and the low frequency X←H⋯Y→ modes is treated within strong anharmonic coupling theory and the relaxation is included following quantum treatment of Rosch and Ratner. The intrinsic anharmonicity of the fast frequency mode is described by a double well potential and of the slow frequency mode by Morse potential. IR spectral density is obtained within the linear response theory by the Fourier transform of the autocorrelation function of the X–H transition dipole moment operator. The main feature brought by the anharmonicity of the H-bond bridge X←H⋯Y→ is the increase of the average frequency of the υX–H IR band with temperature for asymmetrical H-bonds, and decrease for symmetrical and weakly asymmetrical H-bonds.
The numerical results are in fairly good agreement with the experimental behaviour of the first and the second moment of the X–H bands, observed when varying the temperature.
TL;DR: In this paper, the structural and electronic properties of SrZrO3 selected surfaces were investigated by means of density functional theory applied to periodic calculations at B3LYP level.
Abstract: The structural and electronic properties of SrZrO3 selected surfaces were investigated by means of density functional theory applied to periodic calculations at B3LYP level. The relaxation effects for two symmetric and asymmetric terminations are analyzed. The electronic and energy band properties are discussed on the basis of band structure as well density of states. There is a more significant rumpling in the SrO as compared to the ZrO2 terminated surfaces. The calculated indirect gap is 4.856, 4.562, 4.637 eV for bulk, ZrO2 and asymmetric terminations, respectively. The gap becomes direct; 4.536 eV; for SrO termination. The contour in the (110) diagonal plane indicates a partial covalent character between Zr and O atoms for the SrO terminated surface. 2007 Elsevier B.V. All rights reserved.
TL;DR: In this article, the exact analytical solution of the radial Schrodinger equation for the deformed Hulthen and the Morse potentials within the framework of the asymptotic iteration method is presented.
Abstract: We present the exact analytical solution of the radial Schrodinger equation for the deformed Hulthen and the Morse potentials within the framework of the asymptotic iteration method. The bound state energy eigenvalues and corresponding wave functions are obtained explicitly. Our results are in excellent agreement with the findings of the other methods.
TL;DR: In this article, the potential energy (PE) curves for the intramolecular proton transfer in the ground (GSIPT) and excited states of 1-hydroxy-2naphthaldehyde (1H2NA) and 2-hydrox-3-naphthsaldehyde (2H3NA) were studied using DFT/B3LYP(6-31G) and TD-DFT/ B3lyp(6 -31G), respectively.
Abstract: Potential energy (PE) curves for the intramolecular proton transfer in the ground (GSIPT) and excited (ESIPT) states of 1-hydroxy-2naphthaldehyde (1H2NA) and 2-hydroxy-3-naphthaldehyde (2H3NA) were studied using DFT/B3LYP(6-31G) and TD-DFT/ B3LYP(6-31G) level of theory, respectively. Our calculations suggest the non-viability of ground state intramolecular proton transfer for both the compounds. Excited states PE calculations support the ESIPT process to both 1H2NA and 2H3NA. The wide difference in ESIPT emission process of 1H2NA and 2H3NA have been explained in terms of HOMO and LUMO electron density of the enol and keto tautomer of these two compounds. � 2006 Elsevier B.V. All rights reserved.
TL;DR: In this article, the conformational stability of 8-hydroxyquinoline was investigated by density-functional B3LYP calculations using the 6-311++G(d,p) basis set.
Abstract: The conformational stability of the 8-hydroxyquinoline was investigated by density-functional B3LYP calculations using the 6-311++G(d,p) basis set. From the potential energy scans of the internal rotations of the hydroxyl group the calculations predicted a mixture of two conformations, one with the hydroxyl hydrogen pointing to the nitrogen (α-8-hydroxyquinoline) and the other with the hydrogen pointing in the opposite direction (β-8-hydroxyquinoline). The α conformation being about 7.63 kcal/mol more stable than the β. Time-dependent density-functional theory (TD-DFT) was applied to analyze the vertical electronic absorption spectra of α-8-hydroxyquinoline. The 25 lowest excited states were calculated together with the transition dipole moments using the B3LYP/6-311++G(d,p) level of theory. The influence of the conformation on the (hyper)polarizability properties was also investigated.
TL;DR: Theoretical calculations are carried out to predict gas and aqueous phase acidities of a series of 21 carbon acids with pKa values varying from −6.20 to 50.
Abstract: Theoretical calculations are carried out to predict gas- and aqueous-phase acidities of a series of 21 carbon acids with pKa values varying from −6.20 to 50. Acceptable linear correlations (R2 > 0.93, SD
TL;DR: In this paper, a review of electronic aromaticity measures from the perspective of the Huckel molecular orbital (HMO) theory is presented, and the analysis of FLU, PDI, I ring and SCI in the framework of HMO theory provides an interesting scenario for the interpretation of these indices.
Abstract: In this paper, we review the electronic aromaticity measures from the perspective of the Huckel molecular orbital (HMO) theory. The analysis of FLU, PDI, I ring and SCI in the framework of the HMO theory provides an interesting scenario for the interpretation of these indices. Within the Huckel theory the formulas for the Coulson bond orders are easily obtained in a closed form for annulenes, which enables the production of analytical expressions for some of the aromaticity measures. These analytical functions are used to study the ring size dependence of current aromaticity indices. Besides, HMO calculations of polycyclic benzenoids complete the analysis of the electronic aromaticity indices reviewed in this paper, by showing how HMO theory explains the changes in aromaticity due to annulation. All these results help grasping the meaning and the behavior of the electronic aromaticity indices.
TL;DR: In this paper, the hydrogen bonding in solid dispersions of the antihypertension and antianginal drug felodipine, ethylmethyl-4-(2,3-dichlorophenyl)-1,4-dihydro-2,6-dimethyl-3,5-pyridine-dicarboxylate, with the polyvinylpyrrolidone (PVP) or polyethyleneglycol (PEG) water soluble polymers, have been studied at the density functional level of theory with the B3
Abstract: The hydrogen bonding in solid dispersions of the antihypertension and antianginal drug felodipine, ethylmethyl-4-(2,3-dichlorophenyl)-1,4-dihydro-2,6-dimethyl-3,5-pyridine-dicarboxylate, with the polyvinylpyrrolidone (PVP) or polyethyleneglycol (PEG) water soluble polymers, have been studied at the density functional level of theory with the B3LYP exchange correlation functional. Six low energy conformers of felodipine have been located. The vibrational as well as the 1 H and 13 C NMR spectroscopic properties calculated for the most stable isomer were in satisfactory agreement with the experimental data. The hydrogen bonded complexes of felodipine conformers with low molecular weight models of the polymers have been fully optimized. In all cases a N–H⋯O hydrogen bond is formed. The BSSE and ZPE corrected interaction energies were estimated of 30–36 kJ/mol for PVP and 19–21 kJ/mol for PEG complexes. The electron density ( ρ b ) and Laplacian (∇ 2 ρ b ) properties at critical points of the relevant bonds, estimated by AIM calculations, showed that N–H⋯O have low and positive character (∇ 2 ρ b > 0), consistent with electrostatic character of the hydrogen bond. The vibrational study of the hydrogen bonded complexes showed negative (red) shifts for the ν (N–H) stretching mode. Interaction energies, electron density, Laplacian and vibrational data showed a stronger hydrogen bond of felodipine with PVP polymer in comparison to that with PEG, in agreement with experimental data concerning the dissolution rates of the corresponding solid dispersions.
TL;DR: In this paper, an extension of a quantum non-adiabatic treatment of H-bonds involving intrinsic anharmonicity of the fast mode was presented, in order to account for quadratic dependence of both the angular frequency and the equilibrium position of the X H → ⋯ Y stretching mode on the X ← H ⋩ Y → motion, and the effects induced by incorporation of such dependence on the IR spectral density of the high frequency stretching mode.
Abstract: The paper presents extension of a quantum non-adiabatic treatment of H-bonds involving intrinsic anharmonicity of the fast mode [Rekik et al. Chem. Phys. 273 (2001) 11] by accounting for quadratic dependence of both the angular frequency and the equilibrium position of the X H → ⋯ Y stretching mode on the X ← H ⋯ Y → motion, in order to account for stronger H-bonds. Attention is focused on the study of effects induced by incorporation of such dependence on the IR spectral density of the high frequency stretching mode. The spectral density is obtained, within the linear response theory, by Fourier transform of the direct damped autocorrelation function of the dipole moment of the fast stretching mode. The anharmonic coupling between the high frequency X H → ⋯ Y and the low frequency X ← H ⋯ Y → modes is treated by the strong anharmonic coupling theory. Intrinsic anharmonicity of the fast mode is described by a double well potential, whereas the slow mode is considered to be harmonic. The relaxation of the fast mode (direct damping) is considered.
TL;DR: The refined three-dimensional model of the receptor can now be used for docking studies of other ligands, thereby helping the rational design of new drugs for h5-HT4.
Abstract: The serotonin, h5-HT4 receptor is a G protein-coupled receptor (GPCR) known to be involved in a variety of pathological disorders such as irritable bowel syndrome, cardiac atrial arrhythmia and memory deficits. Recent studies have also underlined its potential role in Alzheimer’s disease. We present here the results of molecular dynamics simulations of h5-HT4 receptor binding a non-peptide antagonist ligand in a realistic membrane environment. The GPCR-bound ligand model built in vacuo using homology modelling of bovine rhodopsin and several experimental constraints [L. Rivail, et al., New insights into the human 5-HT4 receptor binding site: exploration of a hydrophobic pocket, Br. J. Pharmacol. 143(3) (2004) 361–370] was relaxed during 10 ns of constant pressure and constant temperature simulation. The results show that the receptor model is stable and that the key interactions formed with the ligand and identified experimentally are conserved. The simulations further reveal that several water molecules migrate from the extracellular milieu toward the putative hydrophobic pocket [L. Rivail, et al., New insights into the human 5-HT4 receptor binding site: exploration of a hydrophobic pocket, Br. J. Pharmacol. 143(3) (2004) 361–370; R. Bureau, et al., Molecular design based on 3D pharmacophore. Application to 5-HT4, J. Chem. Inform. Comput. Sci. (2001) A–F; M.L. Lopez-Rodriguez, et al., Comparative receptor mapping of serotoninergic 5-HT3 and 5-HT4 binding sites. J. Comput. Aided Mol. Des. 11(6) (1997) 589–599] accommodating the ligand, and form a network of interactions with the receptor, hence underlining the limitations of the in vacuo construct. The refined three-dimensional model of the receptor can now be used for docking studies of other ligands, thereby helping the rational design of new drugs for h5-HT4.
TL;DR: In this article, the hybrid DFT methods with 12 different basis sets were used for the computation of FOOF and compared with CCSD/6-311+G* method was made.
Abstract: The hybrid DFT methods with 12 different basis sets were used for the computation of FOOF. Comparison with CCSD/6-311 + G* method was made. The availability and shortcoming of DFT methods for FOOF were pointed out. On that basis, the binary compounds of fluorine and oxygen (O n F m , n = 1–3, m = 1–2) were calculated at the G96PW91/D95(3df) level. The affiliation of lone pair electrons toward the fluorine atom decreases from OF 2 to O 3 F 2 as the number of oxygen increases. The strength of O–O bond decreases from O 2 F 2 to O 3 F 2 . The shorter O–F bond of O 3 F 2 could readily change to longer one and vice versa through a transition state with energy barrier of 11.06 kJ/mol. The O–F bond is much stronger than the O–O bond in O 3 F 2 . On the contrary, the O–F bond is much weaker than the O–O bond in O 2 F 2 . O 2 F and O 3 F can be regarded as weakly bound OO–F and OO–OF adducts, respectively. O 3 F 2 could be regarded as a weakly bound FO–OOF adduct. The standard enthalpies and free energies of formation for the binary compounds were predicted at both the G96PW91 and the G2 levels.
TL;DR: Theoretical calculations were performed to study the nature of the N-H⋯H-B blue-shifted dihydrogen bond in the complex BH3NH3⋮HNO.
Abstract: Theoretical calculations were performed to study the nature of the N–H⋯H–B blue-shifted dihydrogen bond in the complex BH3NH3⋯HNO. The geometric structures and vibrational frequencies of the complex BH3NH3⋯HNO at the MP2/6-31+G(d,p), MP2/6-311++G(d,p), B3LYP/6-31+G(d,p) and B3LYP/6-311++G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. In the N–H⋯H–B dihydrogen bond, the calculated blue shift of N–H stretching frequency is in the vicinity of 130 cm−1. From the natural bond orbital analysis it can be seen that the N–H bond length in the N–H⋯H–B dihydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X–H bond, and the other three factors belong to the bond shortening effects. In the N–H⋯H–B dihydrogen bond, the shortening effects dominate which lead to the blue shift of the N–H stretching frequencies. In addition, solvent effect on the geometric structures, vibrational frequencies and interaction energies of the monomer and complex was studied in detail. It is relevant to the relatively dielectric constants (e).
TL;DR: The rotational transition state in the isomerization of the syn-to-conformer for the parent and substituted benzoic acids has been characterized and the decarboxylation mechanism for these acids was determined.
Abstract: The rotational transition state in the isomerization of the syn- to anti-conformer for the parent and substituted benzoic acids has been characterized and the decarboxylation mechanism for these acids has been determined. A previously unreported intermediate in the salicylic acid decarboxylation pathway has been observed, demonstrating that there is a change in the reaction mechanism when the ortho-group participates in the development of the transition state. The intermediate, in a shallow well, has a keto-like structure. While salicylic acid reacts through the keto-like intermediate, other substituted benzoic acids, including 2-aminobenzoic acid, follow the previously reported direct mechanism.
TL;DR: In this paper, the hydration number of trimethylamine-Noxide (TMAO) and a surfactant dimethyldodecylamine Noxide (DDAO) was investigated.
Abstract: Density functional theory (B3LYP) calculations of the hydration of trimethylamine-N-oxide (TMAO) and a surfactant dimethyldodecylamine-N-oxide (DDAO) are reported. Hydrogen-bonded complexes of DDAO with up to three water molecules and of TMAO with up to five water molecules are studied. Interactions of both TMAO and DDAO with water give rise to the binding energies that are much higher than that in the water dimer. A significant charge transfer from amine oxide to water is observed. Energies of water-water interactions increase in the presence of amine oxides. The hydration number of TMAO in the hydrogen bonded complexes is shown to be three. The energies of amine oxide-water interactions in the hydrogen bonded complexes have been analyzed using differential energetic parameters analogous to the parameters measured in calorimetric experiments.