The electrostatic potential at atomic sites as a reactivity index in the hydrogen bond formation

The paper reviews results from computational studies by molecular orbital and density functional theories on several series of hydrogen bonded complexes. These studies aim at quantifying the reactivity of molecules for the complexation process. Excellent linear relationships are found between the electrostatic potential values at the sites of the electron donor and electron accepting atoms and the energy of hydrogen bond formation (ΔE). The series studied are: (a) complexes of R–CHO and R–CN molecules with hydrogen fluoride; (b) complexes of mono-substituted acetylene derivatives with ammonia; (c) (HCN)_n hydrogen bonded cluster for n=2–7. All 22 studied complexes of carbonyl and nitrile compounds with hydrogen fluoride fall in the same dependence between the energy of hydrogen bond formation and the electrostatic potential at the atomic site of the carbonyl oxygen and nitrile nitrogen atoms, with linear regression correlation coefficient r=0.979. In the case of complexes of mono-substituted acetylene and diacetylene derivatives with NH₃, the correlation coefficient for the dependence between the electrostatic potential at the acidic hydrogen atom and ΔE equals 0.996. For the series of hydrogen bonded (HCN)_n clusters, the correlation coefficient for the relationship between the electrostatic potential at the end nitrogen atom and ΔE is r=0.9996. Similarly, the analogous relationship with the electrostatic potential at the end hydrogen atom has a regression coefficient equal to 0.9994. The dependencies found are theoretically substantiated by applying the Morokuma energy decomposition scheme. The results show that the molecular electrostatic potential at atomic sites can be successfully used to predict the ability of molecules to form hydrogen bonds.     

Complexation of trivalent lanthanide cations by inositol in solid state. The crystal structure and Raman spectra study of NdCl3·inositol·9H2O

The crystal structure of NdCl₃·C₆H₁₂O₆·9H₂O has been determined. It crystallizes in the monoclinic system, p2(1)/n space group with cell dimensions: a=15.824(3) Å, b=8.633(2) Å, c=16.219(3) Å, β=107.24°, V=2116.1(7) ų and Z=4. Each Nd ion is coordinated to nine oxygen atoms, two from inositol and seven from water molecules, with an Nd–O distance of 2.449–2.683 Å, the other two water molecules are hydrogen bonded. No direct contacts exist between Nd and Cl. There is an extensive network of hydrogen bonds in hydroxyl groups, water molecules and chloride ions in the crystal structure of the lanthanide complex. The Raman spectra of Pr–, Nd– and Sm–inositol are similar, which show that the three metal ions have the same coordination mode. The Raman spectra are consistent with their structures.     

A theoretical study of the ground and first excited singlet state proton transfer reaction in isolated 7-azaindole–water complexes

A systematic study of the proton transfer in the 7-azaindole–water clusters (7-AI(H₂O)_n; n=1–4) in both the ground and first excited singlet electronic states is undertaken. DFT(B3LYP) calculations for the ground electronic state shows that the more stable geometry of the initial normal tautomer presents a cyclic set of hydrogen bonds that links the two nitrogen atoms of the base across the waters. For the n=4 cluster the water molecules adopt a double ring structure so that two cycles of hydrogen bonds are found there. From this structure full tautomerization implies only one transition state so that a concerted but non-synchronous process is predicted by our theoretical calculations. This behavior is found both in the ground and the excited states where CIS geometry optimizations and TD(B3LYP) energy calculations are performed. The difference between both states is the height of the energy barrier that is much lower in the excited state. Another clear difference between both electronic states is that full tautomerization is an endergonic process in the ground state whereas it is clearly exergonic (then favorable) in the excited state. This is so because electronic excitation implies a charge transfer from the five-member cycle to the six-member one of 7-azaindole so that the proton transfer from the pyrrolic side to the pyridinic one is favored. These results clearly indicate that full tautomerization will not likely occur in the ground state but it will be quite easy (and fast) in the excited state. Reaction is already feasible in the S₁ 1:1 complex but it is faster in the 1:2 complex. However the reaction slows again for the 1:3 complex and, finally, reaches a new maximum for the largest cluster studied here, the n=4 case. These results, which are in agreement with experimental data, are explained in terms of the number of hydrogen bonds that are involved in the transfer. The proton transfer through a ring formed by the substrate and two water molecules is found to be the more efficient one, at least in this system.     

A density functional study on hydrated clusters of orthoboric acid, B(OH)3(H2O)n (n=1–5)

We have calculated the optimized structures and stabilization energies for hydrated clusters of orthoboric acid molecule, B(OH)₃(H₂O)_n (n=1–5), with a hybrid density functional approach. Although some ion-pair structures are revealed in the case of n=4 and 5 clusters, the most stable structure is found to be a non-proton-transferred form up to n=5 hydrated clusters. The calculated IR spectra of the stable B(OH)₃(H₂O)_n of n=3–5 clusters predict small red shifts of hydrogen-bonded OH frequencies. These geometry and IR results are related to the weak acidity nature of orthoboric acid.     

An ab initio study on the vibrational and electronic spectra of the molybdenum–sulfur clusters with Mo2OnS4−n(n=0–4) core

Using the ab initio method, the vibrational and electronic spectra of binuclear molybdenum clusters which contain Mo₂O_nS_4−n(n=0–4) core were investigated. The main absorption bands in the IR spectra of these clusters are assigned and compared with each other, especially for the case of the trans isomers. The electronic spectra were studied by performing the CIS calculations. The ground state and the first excited state of the clusters were discussed by using the natural bond orbital method. It is shown that the band corresponding to the longest wavelength can be assigned to three kinds of transition types. Two transitions, σ(Mo–Mo)→π*(Mo–X_t)(X=S,O) and σ(Mo–Mo)→σ*(Mo–Mo), can be seen in most cases.     

Local analysis and comparative study of the hydrogen bonds in the linear (HCN)n and (HNC)n clusters

B3LYP/6-311+G(2d,p), the density functional theory method of 98 package, is applied to study the hydrogen bonding of a series of linear (HCN)_n and (HNC)_n molecular clusters (for n=1–10). By the localization analysis methods we developed, pair-wised σ type H-bond orders and bond energies are calculated for each pair of the two near-by molecules in both (HCN)_n and (HNC)_n clusters. The calculated results are checked well with the shortening of N–H or C–H distance, the elongation of CH or NH bond distance, and the red shift of stretching frequencies of CH or NH. All pieces of evidence show that the central pair of the two molecules forms the strongest H bond when n of (HCN)_n or (HNC)_n is even, and the two middle pairs form the two strongest H bonds when n is odd. Two terminal pairs of HCN or HNC molecules always form the two weakest H-bonds in each molecular cluster. When comparing molecular cluster energies between (HCN)_n and (HNC)_n for various values of n, the well-known (HCN)_n is found more stable than the related (HNC)_n from energy calculation. However, if outcomes of H-bond local analysis are contrasted, our analysis significantly shows that inter-molecular H-bonds inside of (HNC)_n clusters are much stronger than the corresponding H-bonds in (HCN)_n with the same n. In comparing energy differences between these related clusters per monomer, [E_(HNC)n−E_(HCN)n]/n is found decreasing monotonically as n increases. All pieces of evidence from this theoretical prediction indicate that (HNC)_n with large n is probably constructed by its relative strong H-bonds.     

Low energy structures of gold nanoclusters in the size range 3–38 atoms

Using a combination of first principles calculations and empirical potentials we have undertaken a systematic study of the low energy structures of gold nanoclusters containing from 3 to 38 atoms. A Lennard-Jones and many-body potential have been used in the empirical calculations, while the first principles calculations employ an atomic orbital, density functional technique. For the smaller clusters (n=3–5) the potential energy surface has been mapped at the ab initio level and for larger clusters an empirical potential was first used to identify low energy candidates which were then optimised with full ab initio calculations. At the DFT-LDA level, planar structures persist up to six atoms and are considerably more stable than the cage structures by more than 0.1 eV/atom. The difference in ab initio energy between the most stable planar and cage structures for seven atoms is only 0.04 eV/atom. For larger clusters there are generally a number of minima in the potential energy surface lying very close in energy. Furthermore our calculations do not predict ordered structures for the magic numbers n=13 and 38. They do predict the ordered tetrahedral structure for n=20. The results of the calculations show that gold nanoclusters in this size range are mainly disordered and will likely exist in a range of structures at room temperature.     

Structure and stability of thiourea with water, DFT and MP2 calculations

The relative stabilities of thiourea in water are investigated computationally by considering thiourea–water complexes containing up to 1–6 water molecules (CS(NH₂)₂(H₂O)_n=1–6) using density functional theory and MP2 ab initio molecular orbital theory. The results show that the thiourea complex is stable and has an unusually high affinity for incoming water molecules. The clusters are progressively stabilized by the addition of water molecules, as indicated by the increasing of the binding energy. The binding energy of the cluster to each H₂O molecule is about 33 kJ mol⁻¹ for n=1–5.The C–S bond, N–C bond distance, Mulliken populations and binding energy keep approximately constant as the clusters increase in size with an increasing number of H₂O molecules. As the solvation progresses, the C–S distance increases monotonically while the Mulliken populations on the C–S bond reduces monotonically with the addition of each H₂O molecule, indicating that the C–S bond of the thiourea unit in the clusters is de-stabilized with an increasing number of H₂O molecules. Charge transfers for the clusters are mainly found at N, S atoms of the thiourea.     

Geometric and energetic properties of Al-doped Sin (n = 2–21) clusters: FP-LMTO-MD calculations

We have investigated the effect of aluminum impurity atoms on the geometric structures and stabilities of neutral and ionic Si_n (n = 2–21) clusters in detail by using full-potential linear-muffin-tin-orbital molecular-dynamics (FP-LMTO-MD) method. Our calculations suggest that most of the ground state structures for neutral and ionic Si_nAl (n = 1–20) clusters can be obtained by substituting one Si atom of their corresponding Si clusters with an Al atom. The neutral Si_n–1Al clusters with one Al atom have similar geometrical configurations to those of the pure Si_n clusters except for local structural distortion. But one Al impurity atom probably reverses the energy ordering of two isomers with small difference. Although, an Al heteroatom reduces the average binding energies for the mixed clusters, it would improve the bond strength between Si atoms in some mixed clusters. Our calculations also suggest that most of the ionic Si_n–1Al clusters adopt the same geometrical configurations as their neutral clusters. But for one selected mixed cluster, the charged structures probably have different energy ordering from the neutral clusters. The anionic Si_n–1Al⁻ clusters, which are isoelectronic to their corresponding pure Si_n clusters, show similar magic behavior.     

Practical dihydroxylation and C–C cleavage of unsaturated fatty acids

Unsaturated fatty acids [C₈H₁₇CH=CH(CH₂)_nCO₂H] (n=7, 11) acids are cleanly dihydroxylated by hydrogen peroxide in the presence of catalytic amounts of H₂WO₄. Under molecular oxygen, in the presence of catalytic amounts of N-hydroxyphthalimide and Co(acac)₃, the diols resulting from erucic (n=11) and oleic (n=7) acid undergo C–C cleavage.     

Radiation yield of oxygen-based radicals in hyperquenched glassy water gamma-irradiated at 77 K

Hyperquenching of liquid water with cooling rates of 10⁶–10⁷ K s⁻¹ yields glassy water. Upon γ-irradiation at 77 K, the only paramagnetic species accumulating in hyperquenched glassy water are the hydroxyl and hydroperoxyl radicals. There are no hydrogen atoms or electrons seen by the ESR technique. For irradiation doses up to about 70 kGy, the relative contributions of hydroxyl and hydroperoxyl radicals to the total amount of paramagnetic species remain virtually constant. The total amount of paramagnetic species, n, is sublinear in dose, d, well approximated by n=8.55×10¹⁶d^0.8 for n in spin g⁻¹ and d in kGy.     

The interaction of fluorosilanes with hydrogen fluoride clusters: strongly blue-shifted hydrogen bonds

The equilibrium structures, binding energies, and vibrational spectra of the complexes formed between hydrogen fluoride clusters (HF)_n (1≤n≤4) and the fluorosilanes SiHF₃, SiH₂F₂, and SiH₃F are investigated within the second-order Møller–Plesset perturbation theory method applying extended basis sets. It is shown that Si–FH–F halogen–hydrogen bonds are formed in the most stable open dimers, SiHF₃–HF, SiH₂F₂HF, and SiH₃FHF. No Si–HF–H hydrogen bonds occur in these dimers. Nevertheless, blue shifts of Si–H stretching frequencies are calculated. All three trimers, fluorosilane–(HF)₂, all three tetramers, fluorosilane–(HF)₃, and two of the pentamers, fluorosilane–(HF)₄, form cyclic structures with strong Si–FH–F halogen–hydrogen bonds and weak Si–HF–H contacts, the latter displaying, nevertheless, strongly blue-shifted Si–H stretching frequencies. These blue shifts are comparable in size to those of the corresponding fluoromethane–(HF)_n complexes and are with about +50 cm⁻¹ for the case n=3 among the largest ever calculated and definitely the largest for Si–H bonds. In the title complexes, the formation of the Si–FH–F halogen–hydrogen bonds induces a substantial stretching of this Si–F bond, which in turn leads to a significant contraction of the fluorosilane Si–H bond in the Si–HF–H hydrogen bond. This disposition of the fluorosilane monomers is demonstrated with the aid of suitable potential energy surface scans and appears to be a prerequisite for the formation of strongly blue-shifted hydrogen bonds.     

Complexes of cationic coinage metal clusters Mn (M=Cu, Ag, Au; n=1–4) and H2S: a theoretical study

Geometries and vibrational frequencies of complexes of cationic coinage metal clusters M_n⁺ (M=Cu, Ag, Au; n=1–4) and H₂S are computed using density functional theory. Thermochemical values for M_n⁺H₂S decomposition channels involving loss of an H atom, H₂ molecule, M atom, or M₂ molecule are also computed. Significantly different results are obtained for closed-shell (n odd) and open-shell (n even) complexes.     

Fluxionality in mixed-metal osmium carbonyl clusters

The heteronuclear clusters [Os₁₀C(CO)₂₄(MPR_3n^m− (n = 1, m = 1; 2: M = Au; 3: M = Ag; 4: M = Cu; 5 n = 2, m = 0, M = Ag) have been prepared. These clusters undergo molecular rearrangements in solution, and two isomeric forms of 2, 3, 4, 5 and 6 have been identified. This interconversion is thought to involve a cap [lrarr2] edge bridge [lrarr2] cap pathway.     

The catalysis of some novel polystyrene-supported porphyrinatomanganese(III) in hydroxylation of cyclohexane with molecular oxygen

Some novel polystyrene-supported porphyrinatomanganese(III) in which alkyl group is bonded to the surface of polystyrene, PS-[Mn(HPTPP)Cl](C_nH_2n+1) (n=2, 6, 8, 18), have been synthesized. Their catalytic activities to hydroxylate cyclohexane in PS-[Mn(HPTPP)Cl](C_nH_2n+1)–O₂–ascrobate system have been found to be higher compared with corresponding non-supported porphyrinatomanganese(III) and increase with the increase of the length of alkyl. These results are discussed in the point of view of metalloporphyrin microenvironment.     

Synthesis and structural behavior of the P-functional organotin chlorides [Ph2P(CH2)3]2SnCl2, Ph2P(CH2)3SnCl2Me, and Ph2P(CH2)nSnCl3 (n=2, 3)

The P-functional organotin dichloride [Ph₂P(CH₂)₃]₂SnCl₂ (3) is synthesized by reaction of Ph₂P(CH₂)₃MgCl with SnCl₄ independently of the molar ratio of the starting compounds. The corresponding organotin trichlorides Ph₂P(CH₂)_nSnCl₂R (4: n=2, R=Cl; 5: n=3, R=Cl; 6: n=3, R=Me) are formed in a cleavage reaction of Ph₂P(CH₂)_nSnCy₃ (n=2, 3) with SnCl₄ or MeSnCl₃, respectively. The main features of the crystal structures of 3–6 are both intra- and intermolecular PSn coordinations and the existence of intermolecular Sn---ClSn bridges. For further characterization of the title compounds, the adducts 4(Ph₃PO)₂ (7) and 5(Ph₃PO) (8), as well as the P-oxides and P-sulfides of 3–6 (9–15), are synthesized. The results of crystal structure analyses of 7, 11, 12, and 14 are reported. The structures of 9–15 are characterized by intramolecular P=XSn interactions (X=O, S). A first insight into the structural behavior of the compounds 3–15 in solution is discussed on the basis of multinuclear NMR data.     

Theoretical investigation on the adsorption of lithium atom on the Sin cluster (n=2–7)

Ab initio calculations are carried out to study the adsorption of Lithium atom on the Si_n cluster with n ranging from 2 to 7. At the MP2/6-31G(d) level, the structures of the neutral Si_n clusters and the Si_nLi clusters (n=2–7) are optimized. The single-point energy at QCISD/6-311+G(d,p) level for the optimized isomers are further performed. Harmonic vibrational frequency analysis at the MP2/6-31G(d) level is also undertaken to confirm that the optimize geometries are stable. Based on our results, the most favorable sites for Li adsorption on the Si_2–7 clusters are the bridge sites. In addition, the vertical ionization energies of the Si_nLi clusters and the electron affinities of the Si_n clusters are also calculated. The clear parallelism between the vertical ionization energies of Si_nLi and the electron affinities of Si_n is found. This is consistent with the fact that the framework of the Si_n in the Si_nLi cluster is similar to the structure of the corresponding negative ion .     

Determination of the first ionization energy of furan (C4H4O) from an extrapolation of two nd Rydberg series observed in the mass-resolved (2 + 1) resonance enhanced multiphoton ionization spectrum

The first ionization energy of furan (C₄H₄O) has been determined from a short extrapolation of two nd (n=6–22) Rydberg series observed in the mass-resolved (2 + 1) resonance enhanced multiphoton ionization spectrum as IE=71673 ± 3 cm⁻¹. This value confirms the higher of the two values in the literature.     

A computational study of bond dissociation enthalpies in haloethenes

Carbon–hydrogen bond dissociation enthalpies (BDEs) were computed for all haloethenes, C₂H_4−nX_n (n=0–3, X=F, Cl, Br, I), at the B3LYP/6-311+G(3df,2p) level using isodesmic reactions. It was found that C–H bond strengths in the monohaloethenes varied substantially, by as much as 18 kJ mol⁻¹, dependent upon the bond's stereochemical position relative to the halogen. BDEs in the dihaloethanes varied in the order CX₂CH–H>(E)-CHXCX–H>(Z)-CHXCX–H. Trends in the computed bond enthalpies were discussed and explained on the basis of relative steric repulsions and hyperconjugative delocalization interactions, as determined from Natural Bond Orbital analysis.     

C CP MAS NMR, FTIR, X-ray diffraction and PM3 studies of some N-(ω-carboxyalkyl)morpholine hydrohalides

N-(ω-carboxyalkyl)morpholine hydrochlorides, OC₄H₈N(CH₂)_nCOOH·HCl, n=1–5, were obtained and analyzed by ¹³C cross polarization (CP) magic angle spinning (MAS) NMR, FTIR and PM3 calculations. The structure of N-(3-carboxypropyl)morpholine hydrochloride (n=3) has been solved by X-ray diffraction method at 100 K and refined to the R=0.031. The crystals are monoclinic, space group P2₁/c, a=14.307(3), b=9.879(2), c=7.166(1) Å, β=93.20(3)°, V=1011.3(3) ų, Z=4. In this compound the nitrogen atom is protonated and two molecules form a centrosymmetric dimer, connected by two N⁺–HCl⁻ (3.095(1) Å) and two O–HCl⁻ (3.003(1) Å) hydrogen bonds. ¹³C CP MAS NMR spectra, contrary to the solution, showed non-equivalence of the ring carbon atoms. The PM3 calculations predict a molecular dimer without proton transfer for an HCl complex, while for an HBr complex an ion pairs with proton transfer, and reproduces correctly the conformation of both dimers but overestimates H-bond distances. Shielding constants calculated from the PM3 geometry of ion pairs gave a linear correlation with the ¹³C chemical shifts in solids.