Density functional theory and topological analysis on the hydrogen bonds in cysteine–propanoic acid complexes

The complexes formed via hydrogen bonding interactions between cysteine and propanoic acid have been studied at the density three-parameter hybrid functional DFT-B3LYP/6-311++G(d,p) level regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis was employed to elucidate the interaction characteristics in cysteine–propanoic acid (Cys–Prop) complexes. More than 10 kinds of hydrogen bonds (H-bonds) including intra- and inter-molecular H-bonds have been found in Cys–Prop complexes. The results show that both the strength of H-bonds and the deformation are important factors for the stability of Cys–Prop complexes. The strongest H-bonds (O2H^A···O1^B and O2H^A···O1^B) exist in the most stable Cys–Prop complex. The stronger H-bonds formed between hydroxyl and O (or N) atom usually stronger than those involve C (or S) atom. Relationships between the electron density (ρ) of BCP and H-bond length as well as the Fock matrix element (F _ij) has also been investigated and used to study the nature of H-bonds. Moreover, the results show that the change of the bond length linearly correlates with the corresponding frequency shift.     

The nature of the C–As bonds in arsaalkynes: an atoms in molecules and electron localization function study

The nature of the C–As bonds present in a series of six neutral and anionic arsaalkynes was investigated. The optimized geometries, vibrational frequencies, and wavefunctions of all the studied species were computed using density functional theory (B3LYP/6-311++G(2d,2p)). To understand the bonding characteristics, Atoms in Molecules theory and topological analysis of the electron localization function were used. For comparison, natural bond orbital analysis was also performed. The results suggest that in five of the six studied compounds, the C–As bonds are essentially triple bonds, with similar characteristics to the C–P analogues in phosphaalkynes.     

Hydrogenation of B 120/? : A Planar-to-Icosahedral Structural Transition in B12H n0/? (n?=?1–6) Boron Hydride Clusters

A systematic density functional theory and wave function theory investigation performed in this work reveals a planar-to-icosahedral structural transition between n = 4–5 in the partially hydrogenated B₁₂H _n ^0/− clusters (n = 1–6) upon hydrogenation of all-boron B₁₂^0/−. Coupled cluster calculations with triple excitations (CCSD(T)) indicate that a distorted icosahedral B₁₂H₆ cluster with C₂ symmetry is overwhelmingly favored (by 35 kcal/mol) over the recently proposed perfectly planar borozene (D_3h B₁₂H₆) (Szwacki et al., Nanoscale Res Lett 4:1085, 2009) which proves to be a high-lying local minimum. A similar 2D–3D structural transition occurs to the corresponding boron boronyl analogues of B₁₂(BO) _n with n –BO terminals. Detailed adaptive natural density partitioning (AdNDP) analyses reveal the bonding patterns of these quasi-planar or cage-like clusters which are characterized with delocalized σ and π molecular orbitals. The electron detachment energies of the concerned anions and excitation energies of the neutrals are also predicted to facilitate their future experimental characterizations.     

Calculation of the hydrogen binding energies of complexes between formamide and adenine-thymine pair

The hydrogen bonding of complexes formed between formamide and adenine-thymine base pair has been completely investigated in the present study. In order to gain deeper insight into structure, charge distribution, and energies of complexes, we have investigated them using density functional theory at 6–311++G(d, p), 6–31G, 6–31+G(d), and 6–31++G(d, p) level. Seven stable cyclic structures (ATF1–ATF7) being involved in the interaction has been found on the potential energy surface. In addition, for further correction of interaction energies between adenine—thymine and formamide, the basis set superposition error associated with the hydrogen bond energy has been computed via the counterpoise method using the individual bases as fragments. The infrared spectrum frequencies, IR intensities and the vibrational frequency shifts are reported.     

DFT study of the structure and stability of Pu(III) and Pu(IV) chloro complexes

The structural characteristics and energies of PuCl _n ^{(3 − n)+} and PuCl _n ^{(4 − n)+} complexes (n = 2–8) have been studied by the density functional theory (DFT) method in the SVWN5 local functional approximation.     

The nature and energy characteristics of intramolecular hydrogen bonds in crystals

The review concerns the results of systematic X-ray diffraction studies of the electron density distribution in the crystals of compounds with strong intramolecular hydrogen bonds N-H...O, O-H...O, O-H...N, and N-H...S. The advantages of the topological analysis of the electron density distribution function in the analysis of the nature and estimation of the H-bond energies directly from experimental data are discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 1–14, January, 2006.     

Electronic structure of alkaline metal hydrides according to MO LCAO-SCF-CNDO cluster calculations

This paper presents the results of a quantum chemical study of compounds MH (M = Li, Na, K, Rb, and Cs) in a cluster approximation. The calculations were performed by the MO LCAO-SCF-CNDO method (special variation which proved to be effective for studying model systems of high-temperature superconductors). The calculation reproduces the expected electron density distribution on the hydrogen and metal atoms in the hydrides as well as the energy characteristics: M-H and M-M bond energ.es and the binding energies of compounds. The latter qualitatively correlate with the bond energies in the series of compounds LiH-CsH. The calculated Fermi energies and forbidden gaps at the Fermi level suggest that in the series being investigated a perfect crystal of lithium hydride will have the highest electric resistance. It is established that the quantum chemical characteristics of the electronic structure of MH change nonmonotonically from Li to Cs. Translated fromZhurnal Strukturnoi Khimii, Vol. 38, No. 3, pp. 431–437, May–June, 1997.     

Assessment of the Van Voorhis–Scuseria exchange–correlation functional for predicting excitation energies using time-dependent density functional theory

We assess the performance of the Van Voorhis–Scuseria exchange–correlation functional (VSXC), a kinetic-energy-density-dependent exchange–correlation functional recently developed in our group, for calculating vertical excitation energies using time-dependent density functional theory in a benchmark set of molecules. Overall, VSXC performs very well, with accuracy similar to that of hybrid functionals such as the hybrid Perdew–Burke–Ernzerhof functional and Becke's three parameter hybrid method with the Lee, Yang, and Parr correlation functional, which contain a portion of Hartree–Fock exchange. Received: 29 December 1999 / Accepted: 5 June 2000 / Published online: 11 September 2000     

Evaluation of the 1-octanol/water partition coefficient of nucleoside analogs via free energy estimated in quantum chemical calculations

The partition coefficients (logP) of nucleoside analogs determined by the difference in the free energies of hydration and solvation in water-saturated octanol using the thermodynamic integration method are reported. The logP values calculated in this approach are closer to the experimental values compared to other ab initio methods. Solvation free energy in water and octanol, free energy of cavity formation in water and Henry’s constants, and some other parameters are estimated at the density functional theory (DFT) and Hartree-Fock level with 6–31G*, 6–31G, and 6–31+G basis sets. Surface area, mass, refractivity, volume, polarizability, and dipole moment are calculated for some drugs with HF and DFT methods. The results show that log P decreases with the decrease in polarizability and the increase in dipole moment.     

Theoretical investigation on the structural and electronic properties of complexes formed by thymine and 2′-deoxythymidine with different anions

Hydrogen bonding interactions between thymine nucleobase and 2′-deoxythymidine nucleoside (dT) with some biological anions such as F⁻ (fluoride), Cl⁻ (chloride), OH⁻ (hydroxide), and NO₃ ⁻ (nitrate) have been explored theoretically. In this study, complexes have been studied by density functional theory (B3LYP method and 6-311++G (d,p) basis set). The relevant geometries, energies, and characteristics of hydrogen bonds (H-bonds) have been systematically investigated. There is a correlation between interaction energy and proton affinity for complexes of thymine nucleobase. The nature of all the interactions has been analyzed by means of the natural bonding orbital (NBO) and quantum theory atoms in molecules (QTAIM) approaches. Donors, acceptors, and orbital interaction energies were also calculated for the hydrogen bonds. Excellent correlations between structural parameter (δR) and electron density topological parameter (ρ _b) as well as between E(2) and ρ _b have been found. It is interesting that hydrogen bonds with anions can affect the geometry of thymine and 2′-deoxythymidine molecules. For example, these interactions can change the bond lengths in thymine nucleobase, the orientation of base unit with respect to sugar ring, the furanose ring puckering, and the C1′–N1 glycosidic linkage in dT nucleoside. Thus, it is necessary to obtain a fundamental understanding of chemical behavior of nucleobases and nucleosides in presence of anions.     

Theoretical study on dithieno[3,2-b:2′,3′-d]phosphole derivatives: high-efficiency blue-emitting materials with ambipolar semiconductor behavior

Phosphole-based systems due to the unique electronic and optical properties have recently been paid much attention as optoelectronic materials. In this work, the relationship among the electronic structure, charge injection, and transport was investigated for five derivatives of dithieno[3,2-b:2′,3′-d]phosphole (systems 1–5). The structures of systems 1–5 in the ground (S₀) and the lowest singlet excited (S₁) states were optimized at the HF/6-31G* and CIS/6-31G* levels of theory, respectively. Based on these structures, electronic spectra were calculated by time-dependent density functional theory. The simulated emission peaks of five phosphole derivatives locating at the blue–green region (448–516 nm), are in good agreement with the experimental data. Compared with tris-(8-quinolinolate) aluminum (III) (Alq₃), normally used as an excellent electron transporter, systems 1–5 show a significant improvement in electron affinity (EA) due to σ*–π* hyperconjugation, which can effectively promote ability of electron injection. The small differences between λ _h and λ _e for systems 1–5 (0.06–0.14 eV) facilitate charge transfer balance, which suggests systems 1–5 can act as potential ambipolar materials. Owing to good rigidity, low-lying LUMO levels, delocalized frontier molecular orbitals, and the small reorganization energies, the five derivatives of dithieno[3,2-b:2′,3′-d]phosphole are expected to be high-efficiency blue materials in single-layer OLEDs.     

Molecular designing and DFT investigation of novel alternating donor–acceptor dibenzo[b,d]thiophen-based systems: from monomer to polymer

The structures and properties of dibenzo[b,d]thiophene (DBT) based alternating donor–acceptor conjugated oligomers, in which thieno[3,4-b]pyrazine (TP), thieno[3,4-b]thiadiazole (TD), and [1,2,5]thiadiazolo[3,4-e]thieno[3,4-b]pyrazine (TTP) as acceptors, and their periodic polymers were investigated by the density function theory (DFT) at the B3LYP/6-31G(d) level. The bond length, electron density at bond critical points (BCPs) and nucleus-independent chemical shift (NICS) are analyzed and correlated with the conductive properties. NICS shows that the conjugation degree is increased with main chain extension. Research results show the conductive ability of compounds with 1:2 D–A ratio is better than that with 1:1 D–A ratio. The reorganization energies and energy bands also are considered. The results suggest that (BTDDBT) _n and (BTPDDBT) _n have small reorganization energy (0.163 and 0.152 eV, respectively) and quite low energy gap (0.73 and 0.56 eV, respectively), which indicate that they may be potential organic conductive materials.     

Combined DFT with NBO and QTAIM studies on the hydrogen bonds in (CH<Subscript>3</Subscript>OH)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 2–8) clusters

The (CH₃OH) _n (n = 2–8) clusters formed via hydrogen bond (H-bonds) interactions have been studied systemically by density functional theory (DFT). The relevant geometries, energies, and IR characteristics of the intermolecular OH···O H-bonds have been investigated. The quantum theory of atoms in molecule (QTAIM) and natural bond orbital (NBO) analysis have also been applied to understand the nature of the hydrogen bonding interactions in clusters. The results show that both the strength of H-bonds and the deformation are important factors for the stability of (CH₃OH) _n clusters. The weakest H-bond was found in the dimer. The strengths of H-bonds in clusters increase from n = 2 to 8, moreover, the strengths of H-bonds in (CH₃OH) _n (n = 4–8) clusters are remarkably stronger than those in (CH₃OH) _n (n = 2, 3) clusters. The small differences of the strengths of H-bonds among (CH₃OH) _n (n = 6–8) clusters indicate that a partial covalent character is attributed to the H-bonds in these clusters. The linear relationships between the electron density of BCP (ρ_b) and the H···O bond length of H-bonds as well as the second-perturbation energies E(2) have also been investigated and used to study the nature of H-bonds, respectively.     

DFT-PCM Study of the Bond Dissociation Energies of N-nitrosoindole Compounds in Acetonitrile

Quantum chemical calculations are used to estimate the equilibrium N–NO bond dissociation energies (BDEs) in acetonitrile (MeCN) for seven N-nitrosoindole compounds. These compounds are studied by employing the hybrid density functional theory (B3LYP, B3P86 and B3PW91) methods together with 6-31G^∗∗ basis sets. The obtained results are compared with the available experimental results. It is demonstrated that the B3PW91 method is the best of these methods to compute the bond dissociation energies of N-nitrosoindole compounds. The solvent effects on the BDEs of the N–NO bond are analyzed and it is shown that the N–NO BDEs in a vacuum, computed by the B3LYP method, are the closest to the computed values in MeCN and the average solvent effect is 4.0 kJ⋅mol⁻¹. The substituent effects on the N–NO BDEs were further analyzed and it is found that the N–NO BDE increases with increments of the Hammett constants of substituent groups on the benzene ring for N-nitrosoindole compounds, except the compound with 5-NO₂−C₈H₅N–NO. Finally, N-nitrosoindole compounds and the other NO-donors (N-nitroso compounds) are compared.     

The calculation of electron localization and delocalization indices at the Hartree–Fock, density functional and post-Hartree–Fock levels of theory

 Localization, λ(A), and delocalization indices, δ(A,B), as defined in the atoms in molecules theory, are a convenient tool for the analysis of molecular electronic structure from an electron-pair perspective. These indices can be calculated at any level of theory, provided that first- and second-order electron densities are available. In particular, calculations at the Hartree–Fock (HF) and configuration interaction (CI) levels have been previously reported for many molecules. However, λ(A) and δ(A,B) cannot be calculated exactly in the framework of Kohn–Sham (KS) density functional theory (DFT), where the electron-pair density is not defined. As a practical workaround, one can derive a HF-like electron-pair density from the KS orbitals and calculate approximate localization and delocalization indices at the DFT level. Recently, several calculations using this approach have been reported. Here we present HF, CI and approximate DFT calculations of λ(A) and δ(A,B) values for a number of molecules. Furthermore, we also perform approximate CI calculations using the HF formalism to obtain the electron-pair density. In general, the approximate DFT and CI results are closer to the HF results than to the CI ones. Indeed, the approximate calculations take into account Coulomb electron correlation effects on the first-order electron density but not on the electron-pair density. In summary, approximate DFT and CI localization and delocalization indices are easy to calculate and can be useful in the analysis of molecular electronic structure; however, one should take into account that this approximation increases systematically the delocalization between covalently bonded atoms, with respect to the exact CI results. Received: 13 February 2002 / Accepted: 24 April 2002 / Published online: 18 June 2002     

DFT studies and AIM analysis of intramolecular N–H···O hydrogen bonds in 3-aminomethylene-2 methoxy-5,6-dimethyl-2-oxo-2,3-dihydro-2λ5-[1,2]oxaphosphinin-4-one and its derivatives

The intramolecular N–H···O hydrogen bonds in 3-aminomethylene-2 methoxy-5,6-dimethyl-2-oxo-2,3-dihydro-2λ⁵-[1,2]oxaphosphinin-4-one and its derivatives (F, H, Li, -BeH) were studied by DFT (density functional theory) methods. The results of calculations were obtained at B3LYP/6-311++G(d,p) level on model species, with the resonance-assisted hydrogen bonds (RAHB). Topological parameters such an electron density, its Laplacian, kinetic electron energy density, potential electron energy density, and total electron energy density at the bond critical points (BCP) of H···O/N–H contact bonds from Bader’s ‘Atoms in molecules’ (AIM) theory were analyzed in details. The energy of the N–H···O interactions studied here was found rather weak (E _HB = 2.53–12.08 kcal/mol). The results of AIM ellipticity indicated π-delocalization over all six atoms within ring.     

An atom-in-molecules and electron-localization-function study of the interaction between O2 and VxOy+/VxOy (x = 1, 2, y = 1–5) clusters

 The most stable structures of V _x O _y ⁺/V _x O _y (x=1, 2, y=1–5) clusters and their interaction with O₂ are determined by density functional calculations, the B3LYP functional with the 6-31G* basis set. The nature of the bonding of these clusters and the interaction with O₂ have been studied by topological analysis in the framework of both the atoms-in-molecules theory of Bader and the Becke–Edgecombe electron localization function. Bond critical points are localized by means of the analysis of the electron density gradient field, ∇ρ(r), and the electron localization function gradient field, ∇η(r). The values of the electron density properties, i.e., electron density, ρ(r), Laplacian of the electron density, ∇²ρ(r), and electron localization function, η(r), allow the nature of the bonds to be characterized, and linear correlation is found for the results obtained in both gradient fields. Vanadium-oxygen interactions are characterized as unshared-electron interactions, and linear correlation is observed between the electron density properties and the V–O bond length. In contrast, O₂ units involve typical shared-electron interactions, as for the dioxygen molecule. Four different vanadium–oxygen interactions are found and characterized: a molecular O₂ interaction, a peroxo O₂ ²⁻ interaction, a superoxo O₂ ⁻ interaction and a side-on O₂ ⁻ interaction. Received: 15 October 2001 / Accepted: 30 January 2002 / Published online: 24 June 2002     

The possibility of the existence of (H2O) n − anions withn=5, 6

Structural changes that occur in cyclic and chain-like water pentamers and hexamers when an electron is added were analyzed at the unrestricted Hartree—Fock level. The vertical and adiabatic electron affinity of the oligomers, the energies of vertical detachment of an electron from the anions (VDE), and the stability of the anions against dissociation into individual water molecules and a free electron were estimated taking into account the second order perturbation theory (MP2) corrections to the energy. All water anions considered are stable against dissociation, but theirVDE values are negative, and only the chain-like hexamer anion has a value ofVDE close to zero, which means metastability of the anion. The energy of attachment of an electron to the oligomers is lower in the case of chain-like structures. The process is accompanied by structure relaxation, which is more substantial for cycles, especially for the cyclic hexamer. In the chain-like anions, the excess electron density is localized on the hydrogen nuclei of that terminal water molecule that acts as an acceptor of the H-bond proton, while in the cyclic anions it is distributed on the orbitals of those free hydrogen atoms that significantly approach each other due to structural relaxation. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 1, pp. 47–53, January 1997     

Structure and thermochromism of spiropyrans. Triplet mechanism of the thermal cleavage/closure of the pyran ring

The spatial and electronic structure and absorption spectra of some representatives of spiropyrans (SP) are calculated in order to study the mechanism of monomolecular chemical reactions. The calculated energies of the triplet states of SP are close to the experimental activation energies of the thermal opening of the pyran ring. The corresponding lowlying electron transitions are localized on the pyran ring, as indicated by spin density distribution in the triplet state. It is concluded that cleavage of SP occurs via the lowest triplet state of SP. For colored open forms of SP having a planar structure, the quantum chemical calculation predicts a transition between the zwitterionic and quinoid states, depending on the character of intermolecular interactions; this transition is accompanied by a significant change in the absorption spectrum. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 5, pp. 787–797, September–October, 199     

Molecular Structure and Conformational Composition of 1-[(Methylthio)methyl]-2-nitrobenzene (MTMNB): A Theoretical and Experimental Study

The conformational composition of gaseous MTMNB and the molecular structures of the rotational forms have been studied by electron diffraction at 130^∘C aided by results from ab initio and density functional theory calculations. The conformational potential energy surface has been investigated by using the B3LYP/6-31G(d,p) method. As a result, six minimum-energy conformers have been identified. Geometries of all conformers were optimized using MP2/6-31G(d,p), B3LYP/6-31G(d,p), and B3LYP/cc-pVTZ methods. These calculations resulted in accurate geometries, relative energies, and harmonic vibrational frequencies for all conformers. The B3LYP/cc-pVTZ energies were then used to calculate the Boltzmann distribution of conformers. The best fit of the electron diffraction data to calculated values was obtained for the six conformer model, in agreement with the theoretical predictions. Average parameter values (r_a in angstroms, angle α in degrees, and estimated total errors given in parentheses) weighted for the mixture of six conformers are r(C–C) = 1.507(5), r(C–C)_{ring, av} = 1.397(3), r(C–S)_av = 1.814(4), r(C–N) = 1.495(4), r(N–O)_av = 1.223(3), ∠(C–C–C)_ring = 116.0–122.5, ∠ C6–C4–C7 = 118.2(4), ∠ C–C–S = 113.6(6), ∠ C–S–C = 98.5(12), ∠ N–C–C4 = 121.9(3), ∠(O–N–C)_av = 116.8(3), ∠ O–N–O = 127.0(4). Torsional angles could not be refined. Theoretical B3LYP/cc-pVTZ torsional angles for the rotation about C–N bond, φ_C−N, were found to be 30.5–36.5^∘ for different conformers. As to internal rotation about C–C and C–S bonds, values of φ_C−C = 68–118^∘ and φ_C−S = 66–71^∘ were obtained for the three most stable conformers with gauche orientation with respect to these bonds. Some conclusions of this work were presented in a short communication in Russ. J. Phys. Chem. 2005, 79, 1701.