Theoretical study of N<Subscript>4</Subscript>X (X = O,S, Se) systems

A series of N₄X (X = O, S, Se) compounds have been examined with ab initio and density functional theory (DFT) methods. To our knowledge, these compounds, except for the C_2v ring and the C_3v towerlike isomers of N₄O, are first reported here. The ring structures are the most energetically favored for N₄X (X = O and S) systems. For N₄Se, the cagelike structure is the most energetically favored. Several decomposition and isomerization pathways for the N₄X species have been investigated. The dissociation of C_2v ring N₄O and N₄S structures via ring breaking and the barrier height are only 1.1 and −0.2 kcal mol⁻¹ at the CCSD(T)/6-311+G*//MP2/6-311+G* level of theory. The dissociation of the cagelike N₄X species is at a cost of 12.1–16.2 kcal mol⁻¹. As for the towerlike and triangle bipyramidal isomers, their decomposition or isomerization barrier heights are all lower than 10.0 kcal mol⁻¹. Although the C_S cagelike N₄S isomer has a moderate isomerization barrier (18.3–29.1 kcal mol⁻¹), the low dissociation barrier (−1.0 kcal mol⁻¹) indicates that it will disappear when going to the higher CCSD(T) level. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Structures and aromaticity of X2Y 2 − (X = C, Si, Ge and Y = N, P, As) anions

The equilibrium geometries, total energies, and vibrational frequencies of anions X₂Y₂ ⁻ (X = C, Si, Ge and Y = N, P, As) are theoretically investigated with density functional theory (DFT) method. Our calculation shows that for C₂N₂ ⁻ species, the D _2h isomer is the most stable four-membered structure, and for other species the C _2v isomer in which two X atoms are contrapuntal is the most stable structure at the B3LYP/6-311 +G_* level. Wiberg bond index (WBI) and negative nucleus-independent chemical shift (NICS) value indicate the existence of delocalization in stable X₂Y₂ ⁻ structures. A detailed molecular orbital (MO) analysis further reveals that stable isomers of these species have strongly aromatic character, which strengthens the structural stability and makes them closely connected with the concept of aromaticity.     

Theoretical insights into the trends in molecular properties of HCY, HSiY and HGeY molecules where Y = N, P, As

To obtain insights into the factors that govern the analogy between HCN and its isostructures, HXY where X = C, Si, Ge and Y = N, P, As, the electronic and structural properties of these species in ground, cationic and anionic states at the QCISD, MP2 and B3LYP levels with 6-311++G** basis set and the first exited state with TD-B3LYP method have been presented. The results suggest that there are some correlations between structural and thermodynamic properties of the smallest member of this group (HCN) and heavier congers. The results of computation at these levels also predict the stability of HCAs in the ground state and HCN, HSiN and HGeN in the cationic state from the energetic point of view. Molecular electrostatic potential map inspection shows that in HXN species nucleophilic region positions on N atom but in HXP and HXAs molecules by increasing the size of central atom nucleophilic region shifts from region near X atom toward terminal atom. Finally, the nature of bonds of HXY moleculs are systematically studied through atoms in molecules (AIM) and natural bond orbital analyses (NBO).     

Interactions between Al12X (X = Al, C, N and P) nanoparticles and DNA nucleobases/base pairs: implications for nanotoxicity

The interactions between neutral Al₁₂X(I _h ) (X = Al, C, N and P) nanoparticles and DNA nucleobases, namely adenine (A), thymine (T), guanine (G) and cytosine (C), as well as the Watson−Crick base pairs (BPs) AT and GC, were investigated by means of density functional theory computations. The Al₁₂X clusters can tightly bind to DNA bases and BPs to form stable complexes with negative binding Gibbs free energies at room temperature, and considerable charge transfers occur between the bases/BPs and the Al₁₂X clusters. These strong interactions, which are also expected for larger Al nanoparticles, may have potentially adverse impacts on the structure and stability of DNA and thus cause its dysfunction.     

Systematic characterization on electronic structures and spectra for a series of complexes, M(IDB)Cl2 (M = Mn, Fe, Co, Ni, Cu and Zn): a theoretical study

Theoretical studies on the coordination stabilities, spectra and DNA-binding trend for the series of metal-varied complexes, M(IDB)Cl₂ (M = Mn, Fe, Co, Ni, Cu and Zn; IDB = N, N -bis(2-benzimidazolylmethyl) amine), have been carried out by using the DFT/B3LYP method and PCM model. The calculated coordination stabilities (S) for these complexes present a trend of S(Ni) > S(Co) > S(Fe) > S(Cu) > S(Zn) > S(Mn). It has been estimated from the molecular orbital energies of the complexes that the DNA-binding affinities (A) of the complexes are in the order of A(Zn) < A(Mn) < A(Fe) ≈ A(Co) < A(Ni) < A(Cu). The studied results indicate that the Cu, Ni and Co complexes with large coordination stabilities present the low virtual orbitals, consequently yielding to the favorable DNA-binding affinities. The spectral properties of excitation energies and oscillator strengths for M(IDB)Cl₂ in the ultraviolet region were calculated by TD-DFT/B3LYP method.     

Multipole electrostatic potential derived atomic charges in NDDO-methods with <Emphasis Type="Italic">spd</Emphasis>-basis sets

The recently introduced multipole approach for computing the molecular electrostatic potential (MEP) within the semiempirical neglect of diatomic differential overlap (NDDO) framework [Horn AHC, Lin Jr-H., Clark T (2005) Theor Chem Acc 114:159–168] has been used to obtain atomic charges of nearly ab initio quality by scaling the semiempirical MEP. The parameterization set comprised a total of 797 compounds and included not only the newly parameterized AM1* elements Al, Si, P, S, Cl, Ti, Zr, and Mo but also the standard AM1 elements H, C, N, O and F. For comparison, the ZDO-approximated MEP was also calculated analytically in the spd-basis. For the AM1*-optimized structures, single-point calculations at the B3LYP, HF and MP2 levels with the 6-31G(d) and LanL2DZP basis sets were performed to obtain the MEP. The regression analysis of all 12 combinations of semiempirical and ab initio MEP data yielded correlation coefficients of at least 0.99 in all cases. Scaling the analytical and multipole-derived semiempirical MEP by the regression coefficients yielded mean unsigned errors below 2.6 and 1.9 kcal mol⁻¹, respectively. Subsequently, for 22 drug molecules from the World Drug Index, atomic charges were computed according to the RESP procedure using XX/6-31G(d) (XX=B3LYP, HF, MP2) and scaled AM1* multipole MEP; the correlation coefficients obtained are 0.83, 0.85 and 0.83, respectively. Figure: Schematic representation of the atomic charge generation: The molecular electrostatic potential (MEP) is calculated using the AM1* Hamiltonian; then the semiempirical MEP is scaled to DFT or ab initio level, and atomic charges are generated subsequently by the restraint electrostatic potential (RESP) fit method. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible to authorized users. Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005.     

Structures of XH4 + and XH6 + (X = B, Al and Ga) Cations

Structures and energies of XH₄ ⁺ and XH₆ ⁺ (X = B, Al and Ga) have been calculated at the density functional theory (DFT) B3LYP/6-311++G(3df,2pd) level. Calculations indicate that although the structure with a three center two electron (3c-2e) bond is the global minimum for BH₄ ⁺, the global minima of AlH₄ ⁺ and GaH₄ ⁺ are not those with one 3c-2e bond, but those with two 3c-2e bonds. For calibration, both structures of AlH₄ ⁺ were also calculated at the ab initio CCSD(T)/cc-pVTZ level and results in agreement with the DFT results were found. Similar calculations also indicate that although the C_2v symmetrical structure with two 3c-2e bonds is the global minimum for BH₆ ⁺, the global minima of AlH₆ ⁺ and GaH₆ ⁺ are not the C_2v symmetrical structures with two 3c-2e bonds but the C₂ symmetrical structures with three 3c-2e bonds.Electronic Supplementary Material available.     

Structures and magnetic properties of mono-doped fullerenes C59Xn and C59X(6mn)m (X=Bm,N+, P+, As+, Si): isoelectronic analogues of C60 and C60(6m)

Structures of mono-doped fullerenes, C59Xn and C59X(6mn)m (X=Bm, N+, P+, As+, Si), the isoelectronic analogues to C60 and C606m with 60 and 66 pi-electrons, have been investigated at the B3LYP/6-31G* level of density functional theory. On the basis of the computed nucleus independent chemical shifts (NICS) at the cage center and also at the center of individual rings as magnetic criteria, heterofullerenes with 60 pi-electrons are as aromatic as the parent C60, while those with 66 pi-electrons are much less aromatic than C606m. The very distinct endohedral chemical shifts of the 66 pi-electron systems may be useful to identify the heterofullerenes through their endohedral 3He NMR chemical shifts.     

The theoretical comparison between two model NO carriers, MeSNO and MeSeNO

In this study, we apply a hybrid DFT functional, MPW1LYP, to make a comparison between MeSNO and MeSeNO. Due to the mesomeric effect and negative hyperconjugation, Se-nitrososelenols seem to be more unstable than S-nitrosothiols regarding unimolecular decomposition. Interestingly, however, the barrier of the transnitrosation reaction of MeSeNO is larger than that of MeSNO, disregarding nucleophiles in the gas phase. Using the polarizable continuum model to consider the water solvent effect, the transnitrosation reactions of MeXNO and YMe⁻ (X = S, Se; Y = S, Se) are found to undergo concerted reactions, in sharp contrast to the two-step reaction pathways concluded in the gas phase. Moreover, the barriers of the transnitrosation reactions of MeSNO for nucleophiles SMe⁻ and SeMe⁻ from the gas phase to the aqueous solution are found to be decreased, while the transnitrosation reactions of MeSeNO are essentially barrierless in aqueous solution.     

Theoretical characterization of SOME amides and esters DERIVATIVES of valproic acid

The equilibrium structures, the planarity of the C(=O)X linkage and the nature of the chemical bond in the Y−C(=O)−XR₁R₂ [where: Y= −CH−(CH₂−CH₂−CH₃)₂, X=N,O and R₁, R₂= H; alkyl and aryl groups and lone pair electrons (lp)] molecular fragment of derivates of Valproic acid (Vpa) with antiepileptic activity were studied systematically by means of B3LYP calculations and topological analysis of the electron localization function (ELF). The covariance parameter cov[Ω_i, Ω_j] reveals a dominating delocalization effect between the lone pair V(O₁), V(X) and the electron density of the H−C and H−X₁ bonds resulting from the existence of not only non-conventional intramolecular hydrogen bonding patterns as C−H...O/N but also a weak closed-shell stabilizing interaction type arising from a dihydrogen bonding as C−H...H−N, where H...H contacts at a significantly shorter distance than twice the hydrogen atom van der Waals radius. The analyzed data derived from ELF domains were found to be in agreement with the known features and properties of the hydrogen bonding interactions discussed in this work.     

A theoretical study on the coordination behavior of some phosphoryl,carbonyl and sulfoxide derivatives in lanthanide complexation

The selectivity of phosphoryl P(O)R₃, sulfoxide S(O)R₂, and carbonyl C(O)R₂ (R?=?NH₂, CH₃, OH, and F) derivatives with lanthanide cations (La³⁺, Eu³⁺, Lu³⁺) was studied by density functional theory calculations. Theoretical approaches were also used to investigate energy and the nature of metal–ligand interaction in the model complexes. Atoms in molecules and natural bond orbital (NBO) analyses were accomplished to understand the electronic structure of ligands, L, and the related complexes, L–Ln³⁺. NBO analysis demonstrated that the negative charge on phosphoryl, carbonyl, and sulfoxide oxygen (O_P, O_C, and O_S) has maximum and minimum values when the connected –R groups are –NH₂ and –F. The metal–ligand distance declines as, –F?>?–OH?>?–CH₃?>?–NH₂. Charge density at the bond critical point and on the lanthanide cation in the L–Ln³⁺ complexes varies in the order –F?<?–OH?<?–CH₃?<?–NH₂, due to greater ligand to metal charge transfer, which is well explained by energy decomposition analysis. It was also illustrated that E⁽²⁾ values of Lp(N)?→?σ*(Y–N) vary in the order P=O ? S=O ? C=O and the related values of Lp(N)?→?σ*(Y=O) change as C=O ? S=O ? P=O in (NH₂)_nYO ligands (Y?=?P, C, and S). Trends in the L–Ln³⁺ CP–corrected bond energies are in good accordance with the optimized O_Y?Ln distances. It seems that, comparing the three types of ligands studied, NH₂–substituted are the better coordination ligands.

Open image in new window

Graphical Abstract Density functional theory (B3LYP) calculations were used to compare structural, electronic and energy aspects of lanthanide (La, Eu, Lu) complexes of phosphine derivatives with those of carbonyls and sulfoxides in which the R– groups connected to the P=O, C=O and S=O are –NH₂, –CH₃, –OH and –F.

     

Hydrogen bonding interactions in PN···HX complexes: DFT and ab initio studies of structure, properties and topology

Spin-restricted DFT (X3LYP and B3LYP) and ab initio (MP2(fc) and CCSD(fc)) calculations in conjunction with the Aug-CC-pVDZ and Aug-CC-pVTZ basis sets were performed on a series of hydrogen bonded complexes PN···HX (X = F, Cl, Br) to examine the variations of their equilibrium gas phase structures, energetic stabilities, electronic properties, and vibrational characteristics in their electronic ground states. In all cases the complexes were predicted to be stable with respect to the constituent monomers. The interaction energy (ΔE) calculated using a super-molecular model is found to be in this order: PN···HF > PN···HCl > PN···HBr in the series examined. Analysis of various physically meaningful contributions arising from the Kitaura-Morokuma (KM) and reduced variational space self-consistent-field (RVS-SCF) energy decomposition procedures shows that the electrostatic energy has significant contribution to the over-all interaction energy. Dipole moment enhancement (Δμ) was observed in these complexes expected of predominant dipole-dipole electrostatic interaction and was found to follow the trend PN···HF > PN···HCl > PN···HBr at the CCSD level. However, the DFT (X3LYP and B3LYP) and MP2 levels less accurately determined these values (in this order HF < HCl < HBr). Examination of the harmonic vibrational modes reveals that the PN and HX bands exhibit characteristic blue- and red shifts with concomitant bond contraction and elongation, respectively, on hydrogen bond formation. The topological or critical point (CP) analysis using the static quantum theory of atoms in molecules (QTAIM) of Bader was considered to classify and to gain further insight into the nature of interaction existing in the monomers PN and HX, and between them on H-bond formation. It is found from the analysis of the electron density ρ _c , the Laplacian of electron charge density ∇²ρ_c, and the total energy density (H _c ) at the critical points between the interatomic regions that the interaction N···H is indeed electrostatic in origin (ρ_c > 0, ∇²ρ_c > 0 and H_c > 0 at the BCP) whilst the bonds in PN (ρ_c > 0, ∇²ρ_c > 0 and H_c < 0) and HX ((ρ_c > 0, ∇²ρ_c < 0 and H_c < 0)) are predominantly covalent. A natural bond orbital (NBO) analysis of the second order perturbation energy lowering, E⁽²⁾, caused by charge transfer mechanism shows that the interaction N···H is n(N) → BD*(HX) delocalization.     

Insight into the lithium/hydrogen bonding in (CH<Subscript>2</Subscript>)<Subscript>2</Subscript>X...LiY/HY (X: C=CH<Subscript>2</Subscript>, O,S; Y=F,Cl, Br) complexes

The nature of the lithium/hydrogen bonding between (CH₂)₂X(X: C=CH₂, O, S) and LiY/HY(Y=F, Cl, Br) have been theoretically investigated at MP2/6-311++G (d, p) level, using Bader’s “atoms in molecules (AIM)” theory and Weinhold’s “natural bond orbital (NBO)” methodology. The molecule formation density differences (MFDD) of the titled complexes are analyzed. Two kinds of geometries of the lithium/hydrogen bonded complexes are compared. As a whole, the nature of lithium bond and hydrogen bond are different. For the same electron donor and the same acceptor, lithium bond is stronger than hydrogen bond. For the same electron acceptor and different kind of donors, the interaction energies follows the n-type> π-type > pseudo-π-type order. For the same (CH₂)₂X, the interaction energy increases in the sequence of Y=F, Cl and Br for lithium bond systems while it decreases for hydrogen bond systems. Electron transfer plays an important role in the formation of lithium bond systems while it is less important in the hydrogen bond systems.     

Studies of silyl and germyl group VI species. Part VIII. Synthesis and characterization of trimethyl-, silyl-, germyl- and stannyl-methyl derivatives of methane- and benzene-selenols

Asymmetrically substituted selenides of the type (CH₃)₃MCH₂SeR, where M = Si, Ge, Sn and R = CH₃ and C₆H₅, have been prepared by the reaction of Group IV halides with lithium organoselenolates and characterized by their infra-red, Raman, ¹H, ¹³C and ⁷⁷Se (M = Si, Ge) NMR spectra.     

Growth and fruitbody formation ofGanoderma lucidum on media supplemented with vanadium, selenium and germanium

Responses of mycelia ofGanoderma lucidum to vanadium, selenium and germanium were examined over a wide range of concentrations (10–1, 120 μg/ml) in pure culture. Se and V were found to be highly toxic, but Ge was not toxic at the levels tested.Ganododerma lucidum cultivated on substrates of sawdust with V (30–80 μg/g) developed mature fruitbodies, but the bioaccumulation of V was quite low (2.5–7 μg/g in pileus, 12.5–21.5 μg/g in stipe and <1 μg/g in basidiospores). Se as Na₂SeO₄ labeled with⁷⁵Se was effectively taken up from substrates and accumulated in fruitbodies (mainly in pileus), then depleted by discharge of basidiospores. Ge as GeCl₄ labeled with⁷⁷Ge was easily uptaken and translocated into fruitbodies.     

The P2X1 receptor and platelet function

Extracellular nucleotides are ubiquitous signalling molecules, acting via the P2 class of surface receptors. Platelets express three P2 receptor subtypes, ADP-dependent P2Y1 and P2Y12 G-protein-coupled receptors and the ATP-gated P2X1 non-selective cation channel. Platelet P2X1 receptors can generate significant increases in intracellular Ca²⁺, leading to shape change, movement of secretory granules and low levels of α_IIbβ₃ integrin activation. P2X1 can also synergise with several other receptors to amplify signalling and functional events in the platelet. In particular, activation of P2X1 receptors by ATP released from dense granules amplifies the aggregation responses to low levels of the major agonists, collagen and thrombin. In vivo studies using transgenic murine models show that P2X1 receptors amplify localised thrombosis following damage of small arteries and arterioles and also contribute to thromboembolism induced by intravenous co-injection of collagen and adrenaline. In vitro, under flow conditions, P2X1 receptors contribute more to aggregate formation on collagen-coated surfaces as the shear rate is increased, which may explain their greater contribution to localised thrombosis in arterioles compared to venules within in vivo models. Since shear increases substantially near sites of stenosis, anti-P2X1 therapy represents a potential means of reducing thrombotic events at atherosclerotic plaques.     

<Emphasis Type="Italic">Ab initio</Emphasis> DFT study of bisphosphonate derivatives as a drug for inhibition of cancer: NMR and NQR parameters

DFT computations were carried out to characterize the ¹⁷Oand ²H electric field gradient, EFG, in various bisphosphonate derivatives. The computations were performed at the B3LYP level with 6-311++G (d,P) standard basis set. Calculated EFG tensors were used to determine the ¹⁷O and ²H nuclear quadrupole coupling constant, χ and asymmetry parameter, η. For better understanding of the bonding and electronic structure of bisphosphonates, isotropic and anisotropic NMR chemical shieldings were calculated for the ¹³C, ¹⁷O and ³¹P nuclei using GIAO method for the optimized structure of intermediate bisphosphonates at B3LYP level of theory using 6-311++G (d, p) basis set. The results showed that various substituents have a strong effect on the nuclear quadrupole resonance (NQR) parameters (χ, η) of ¹⁷O in contrast with ²H NQR parameters. The NMR and NQR parameters were studied in order to find the correlation between electronic structure and the activity of the desired bisphosphonates. In addition, the effect of substitutions on the bisphosphonates polarity was investigated. Molecular polarity was determined via the DFT calculated dipole moment vectors and the results showed that substitution of bromine atom on the ring would increase the activity of bisphosphonates.     

Aromatic C20F20 cage and its endohedral complexes X@C20F20 (X = H-, F-, Cl-, Br-, H, He)

The structure and stability of endohedral X@C₂₀F₂₀ complexes (X = H⁻, F⁻, Cl⁻, Br⁻, H, He) have been computed at the B3LYP level of theory. All complexes in I _h symmetry were found to be energy minimum structures. H⁻@C₂₀F₂₀ and F⁻@C₂₀F₂₀ complexes have negative inclusion energies, while other complexes have positive inclusion energies. Similarity between C₂₀F₂₀ and C₂₀H₂₀ has been found for X = H and He. On the basis of the computed nucleus independent chemical shift values at the cage center, both C₂₀F₂₀ and C₂₀F₂₀ are aromatic. Figure Endohedral X@C₂₀F₂₀ complexes     

Electronic spectra of the chromium chalcocarbonyl complexes,Cr(CO)5(CX) and (η6-C6H6)Cr(CO)2(CX) (X= O,S,Se)

The room-temperature electronic spectra of the chromium chalcocarbonyl complexes, Cr(CO)₅(CX) and (η⁶-C₆H₆)Cr(CO)₂(CX) (X = O, S, Se), have been recorded in solution, and in some cases, in the gas phase. Assignments for the thiocarbonyl and selenocarbonyl spectra are proposed on the basis of the literature assignments for the parent all-CO derivatives. Overall, the data support the order of increasing electron withdrawing capacity of the chalcocarbonyl ligands as CO < CS < CSe.     

Theoretical investigations into the intermolecular hydrogen-bonding interactions of <Emphasis Type="Italic">N</Emphasis>-(hydroxymethyl)acetamide dimers

The structures of the N-(hydroxymethyl)acetamide (model molecule of ceramide) dimers have been fully optimized at B3LYP/6–311++G** level. The intermolecular hydrogen bonding interaction energies have been calculated using the B3LYP/6–311++G**, B3LYP/6–311++G(2df,2p), MP2(full)/6–311++G** and MP2(full)/6–311++G(2df,2p) methods, respectively. The results show that the O–H···O, N–H···O, O–H···N, and C–H···O hydrogen bonding interactions could exist in N-(hydroxymethyl)acetamide dimers, and the O–H···O, N–H···O, and O–H···N hydrogen bonding interactions could be stronger than C–H···O. The three-dimensional network structure formed by ceramide molecules through intermolecular hydrogen bonding interactions may be the main reason why the stratum corneum of skin could prevent foreign substances from entering our body, as is in accordance with the experimental results. The stability of hydrogen-bonding interactions follow the order of (a)?>?(b)?≈?(c)?>?(d)?>?(e)?≈?(f)?>?(g)?>?(h). The analyses of the energy decomposition, frequency, atoms in molecules (AIM), natural bond orbital (NBO), and electron density shift are used to further reveal the nature of the complex formation. In the range of 263.0–328.0 K, the complex is formed via an exothermic reaction, and the solvent with lower temperature and dielectric constant is favorable to this process.

Open image in new window

Graphical abstract The structures and the O–H···O=C, N–H···O=C and C–H···O=C H-bonding interactions in the N-(hydroxymethyl)acetamide (model molecule of ceramide) dimers were investigated using the B3LYP and MP2(full) methods.