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.     

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.     

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.     

Excess electrons as a probe for polar “fluid structure”

The transition of excess electrons from the quasi-free to the localized state in subcritical and supercritical ammonia vapour was observed in the density range from about 5.6 × 10⁻² to 1 × 10⁻¹ g/cm³. In the same density range, the Kirkwood correlation factory g as a measure of orientational correlation of ammonia molecules, has its strongest density dependence. From this fact and other experimental data on localized (solvated) electrons in sub- and super-critical ammonia, it is concluded that the excess electron is a proper probe to study polar fluid structure.     

First principles study of the structure, electronic state and stability of SinCm anions

Structure, electronic state and energy of Si_nC⁻ and Si_nC⁻₂ (n=1–7) anions have been investigated using the density functional theory. Structural optimization and frequency analysis are performed at the level B3LYP/6-311G(d). The charged-induced structural changes in these anions have been discussed. The strong C–C bond is also favored over C–Si bonds in the Si_nC⁻_m anions in comparison with corresponding neutral cluster. Among different Si_nC⁻ and Si_nC⁻₂ (n=1–7) anions, Si₃C⁻, Si₅C⁻ and Si₂C⁻₂ are most stable. Their stability has a decreasing tendency with the increase in the size of these clusters.     

DFT studies on coplanar poly-cage cubanes C8+4nH8 (n=1–5)

Coplanar poly-cage cubanes C_8+4nH₈ (n=1–5) have been studied using DFT method at B3LYP/D95** level of theory, vibrational frequencies of these molecules have been calculated at B3LYP/D95** level of theory and spectrums of these molecules have been simulated else, heats of formation of these molecules also have been estimated here.     

Infrared band-shape analysis and hydrogen-bonding dynamics of the HCOOH low-temperature crystal

The infrared OH-stretching band shape of crystalline formic acid (HCOOH) at low temperature is analyzed on the ground of a recent theory involving a semiclassical approximation for the evolution operator. The adiabatic potential function for the slow OO stretching mode (N coordinate) is computed from the observed spectrum for the excited state of the fast ν_OH vibration (n coordinate) and is compared with that derived from a time-independent approach. Both theories are consistent with Morse-type potentials and a large shortening of the hydrogen bond in the excited state. The dipole moment operator appears to be N independent. An additional coupling between n and an external OO bending coordinate of the hydrogen bond which manifests itself as a Franck—Condon progression of the ν_OH mode is introduced to account for the observed band manifold. The structure and the dynamics of formic acid in the ground and upper states of the ν_OH vibration are discussed and compared with those previously obtained for similar moderately strong hydrogen-bonded systems.     

Viscometric and sorption equilibrium studies on n-alkane-butanone-poly-(dimethylsiloxane) systems

Intrinsic viscosities, [η], second virial coefficients, A₂, and preferential solvation coefficients, λ, for the ternary systems n-alkane (l)-butanone (2)-poly(dimethylsiloxane) (PDMS) (3), with n-alkane = n-hexane, n-heptane, n-nonane and n-undecane, have been determined at 20°. The K and a constants of the Mark-Houwink equation have been evaluated over the whole composition range of the binary solvent mixtures. Polymer (mixed solvent) interaction parameters and unperturbed dimensions have been evaluated both from A₂ and [η] data, the feasibility of A₂ evaluation from [η] experimental data or vice versa being discussed. Experimental and calculated (through Dondos and Patterson theory) excess free energies, G^E, follow similar trends with composition; large numerical discrepancies, however, arise between both sets of G^E. Maxima in [η], in a and in A₂ are accompanied by inversion points in λ. The solvent mixture composition range in which PDMS is preferentially solvated by n-alkane, as well as the extent of solvation, decrease with increasing number of carbon atoms in the n-alkane.     

Synthesis, crystal structure and third-order non-linear optical property of heterobimetallic cluster compound [MoOICu3S3(2,2′-bipy)2]

Nest-shaped cluster [MoOICu₃S₃(2,2′-bipy)₂] (1) was synthesized by the treatment of (NH₄)₂MoS₄, CuI, (n-Bu)₄NI, and 2,2′-bipyridine (2,2′-bipy) through a solid-state reaction. It crystallizes in monoclinic space group P2₁/n, a=9.591(2) Å, b=14.820(3) Å, c=17.951(4) Å, β=91.98(2)°, V=2549.9(10) ų, and Z=4. The nest-shaped cluster was obtained for the first time with a neutral skeleton containing 2,2′-bipy ligand. The non-linear optical (NLO) property of [MoOICu₃S₃(2,2′-bipy)₂] in DMF solution was measured by using a Z-scan technique with 15 ns and 532 nm laser pulses. The cluster has large third-order NLO absorption and the third-order NLO refraction, its ₂ and n₂ values were calculated as 6.2×10⁻¹⁰ and −3.8×10⁻¹⁷ m² W⁻¹ in a 3.7×10⁻⁴ M DMF solution.     

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 molecular level study of the aqueous microsolvation of acetylene

We present an analysis of the structural, energetic and spectral features associated with the different hydrogen bonded networks found in the first few acetylene–water clusters AW_n (n=1–4) from first principles calculations. Contrary to the predictions of an empirical interaction potential, acetylene is incorporated into a hydrogen bonded ring when it clusters with two or three water molecules. This structural pattern changes for n=4 with the formation of a water tetramer interacting with acetylene. This structural transition from n=3 to 4 is spectroscopically manifested by a qualitative change in the appearance of the infrared spectra of the corresponding global minima.     

General theoretical analysis of four-connected polyhedral molecules

Molecular orbital calculations on four-connected polyhedral molecules have resulted in the following generalisations. Spherical four-connected transition metal carbonyl polyhedra are characterised by 14n + 2 electrons and their Main Group analogues by 4n + 2 electrons. Non-spherical four-connected polyhedra have variable electron counts of 14n to 14n + 4 (or 4n to 4n + 4). These generalisations have been analysed in terms of Stone's Tensor Surface Harmonic Theory. The development of electron counting rules for condensed polyhedra derived from four-connected polyhedral fragments is also described.     

Energy transfer to a morse oscillator

The vibrational excitation of a Morse oscillator in a collinear collision is determined analytically using a new dynamical algebra. The dependence of V → T processes on the initial vibrational state is examined. At finite coupling strengths the decline of P_n → _n−1/n with n is faster than that derived for weak coupling.     

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 .     

The ‘triplet-excited region’ in linear polyenes: Real or artifactual?

The geometries for the planar T₁ states of linear polyenes C_nH_n+2 (n=8, 10, 12, 14, 16, 18, 20, and 22) were optimized by ab initio SCI calculations. It was found that the bond alternation which existed in the S₀ state disappears only in the central region of the polyene chain. This is quite similar to the ‘triplet-excited region’ which was observed in PPP SDCI calculations for decapentaene (n=10), tetradecaheptaene (n=14), octadecanonaene (n=18), and docosaundecaene (n=22) (M. Kuki, Y. Koyama, N. Nagae, J. Phys. Chem. 95 (1991) 7171). However, CASSCF calculations performed for octatetraene (n=8) gave considerably different geometries from the SCI geometries. The reason for this is discussed and we conclude that the appearance of the ‘triplet-excited region’ in SCI and SDCI calculations is artifactual.     

The half projected Hartree-Fock function for determining singlet excited states. Application to cyclobutanone and 3-cyclopenten-1-one

The Half-Projected-Hartree-Fock procedure (HPHF) for determining singlet ground states is briefly described and extended to the direct determination of singlet excited states. The procedure is applied, using a [7s,3p/2s,1p] basis set, to determine the optimal geometry of two relatively large molecules, to which large CI calculations cannot be easily applied. These two molecules are cyclobutanone and 3-cyclopenten-1-one in their lowest singlet (n → π) excited state. Both molecules are found to exhibit in their excited state a pyramidal structure with the carbonyl oxygen atom pointing outward from the molecular plane. RHF calculations for the singlet ground state were also performed for comparison. The theoretical geometrical parameters compare well with the experimental data.     

A theoretical study of protonated OCnOH ions, n=3–8

Since ion-neutral reactions are a major component of the processes driving interstellar chemistry, most reaction network include protonated species. Besides, these ions are able to initiate chemical processes that would not occur with their neutral parents. In this contribution we report a systematic study of the protonated adducts of the OC_nO series (n=3–8) using the B3LYP level of theory. The structures of all possible O-protonated and C-protonated isomers of [OC_nOH⁺] have been determined together with their rotational constants, vibrational frequencies and intensities. Although it appears that these ions belong to two different series, odd-n and even-n, it is found that protonation occurs at the carbons second to the terminal oxygens for all n. The most stable structure is found to be the singlet ion whatever the singlet or triplet spin state of the parent species. However, due to the lack of efficient spin–orbit coupling, only the odd series [OC_nOH⁺] with n=3,5,7 should be formed on the singlet ground state surface. Analysis of the infrared intensities shows that the spectra are dominated by only one or two very strong bands (CC stretching) that carry most of the overall intensity in the 2200–2350 cm⁻¹ region.     

Density functional theory analysis of CaRgn complexes: (Rg=He, Ne, Ar; n=1–4)

CaRg_n⁺ (Rg=He, Ne, Ar) complexes with n=1–4, are investigated by performing using the B3LYP/6-311+G (3df) density functional theory calculations. The CaHe_n⁺ (n=1–4) complexes are found to be stable. In the case of CaNe_n⁺ and CaAr_n⁺, stable structures and stationary point were found only for n=1 and 2. For n=3 in the C_3V and the D_3h point group as well as for n=4 in the T_d (tetrahedral) point group a saddle point (imaginary frequency) is observed and global minimum could be obtained along the potential energy surface.     

A piezoelectric quartz crystal sensor array self assembled calixarene bilayers for detection of volatile organic amine in gas

P-tert-butylcalix[n]arenes (n=4, 6, 8, abbreviated as CA[4], CA[6], CA[8], respectively) were immobilized on the Au surface of the piezoelectric quartz crystal by the reaction between CA[n] and the acid chloride terminated mercaptoacetic acid (MAA) self assembled monolayers to form MAA/CA[n] bilayers. The sensing films were not only immobilized easily and reproducibly, but also used to improve the reversibility of the sensor signal. The response characteristics show the response of CA to organic amine attributes to specific interaction between CA[n] (host) and organic amines (guest). The frequency shifts of n-butylamine and iso-butylamine are much larger than tert-butylamine and diethylamine because of shape-selection and hydrogen bonding. Compared to CA[6] and CA[4], CA[8] has highest sensitivity to organic amine due to having more flexibility to accommodate guest molecules. A sensor array with three-layer back-propagation neural network was applied to detect the binary mixture of n-butylamine in the range of 7.14–142 μl l⁻¹ and iso-butylamine in the range of 7.14–57 μl l⁻¹. The optimum values of learning rate (0.15) and momentum term (0.8) were determined by experiment. The best epoch of training was 1098. The root mean square error of prediction was 1.69 (μl l⁻¹) for n-butylamine, and 1.42 (μl l⁻¹) for iso-butylamine.