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The water hexamer is known to have a number of isoenergetic structures. The first experimental identification of the O–H stretching vibrational spectra of the water hexamer was done in the presence of benzene. It was followed by the identification of the pure water hexamer structure by vibration-rotational tunneling (VRT) spectroscopy. Although both experiments seem to have located only the Cage structure, the structure of the benzene–water hexamer complex is not clearly known, and the effect of benzene in the water hexamer is unclear. In particular, it is not obvious how the energy difference between nearly isoenergetic water hexamer conformers changes in the presence of benzene. Thus, we have compared the benzene complexes with four low-lying isoenergetic water hexamers, Ring, Book, Cage, and Prism structures, using ab initio calculations. We also investigated the effects of the presence of benzene on the structures, harmonic vibrational frequencies, and infrared (IR) intensities for the four low-lying energy conformers. There is little change in the structure of the water hexamer upon its interaction with the benzene molecule. Hence the deformation energies are very small. The dominant contribution to the benzene–water cluster interaction mainly comes from the π–H interactions between benzene and a single water molecule. As a result of this π–H interaction, O–Hπ bond length increases and the corresponding stretching vibrational frequencies are redshifted. The IR spectral features of both (H2O)6 and benzene–(H2O)6 are quite similar. From both the energetics and the comparison of calculated and experimental spectra of the benzene–(H2O)6, the water structure in these complexes is found to have the Cage form. In particular, among the four different Cage structures, only one conformer matches the experimental O–H vibrational frequencies.

The correlation of various properties of water clusters (H2O)n=1–10 to the cluster size has been investigated using extensive ab initio calculations. Since the transition from two dimensional (2-D) (from the dimer to pentamer) to 3-D structures (for clusters larger than the hexamer) is reflected in the hexamer region, the hexamer can exist in a number of isoenergetic conformers. The wide-ranging zero-point vibrational effects of the water clusters having dangling H atoms on the conformational stability by the O–H flapping or proton tunneling through a small barrier (∼0.5 kcal/mol) between two different orientations of each dangling H atom are not large (∼0.1) kcal/mol). Large dipole moments (>2.5 D) are found in the dimer and decamer, and significant dipole moments (∼2 D) are observed in the monomer, hexamer, and nonamer. The polarization per unit monomer rapidly increases with an increasing size of the cluster. However, this increase tapers down beyond the tetramer. The O–H vibrational frequencies serve as sensitive indicators of the status of proton donation (“d”) and acceptance (“a”) (i.e., the structural signature of H-bond type) for each water monomer in the cluster. In general, the magnitudes of the O–H frequencies (ν) for each cluster can be arranged in the following order: ν3da (single donor–single acceptor) ≅ν3daa (single donor–double acceptor) >ν3dda (double donor–single acceptor) >ν1dda>ν1da> (or ≅) ν1daa. The increase in the cluster size has a pronounced effect on the decrease of the lower frequencies. However, there are small changes in the higher frequencies (ν3da and ν3daa). The intensities of ν1daa and ν1da are very high, since the increased atomic charges can be correlated to the enhanced H-bond relay effect. On the other hand, the intensities of the ν1dda modes are diminished by more than half. Most of the above data have been compared to the available experimental data. Keeping in view the recent experimental reports of the HOH bending modes, we have also analyzed these modes, which show the following trend: ν2dda>ν2daa≅ν2da. The present study therefore would be useful in the assignments of the experimental O–H stretching and HOH bending modes.

The interaction of the water dimer with both the olefinic and aromatic π systems (ethene, benzene, toluene, fluorobenzene, and p-difluorobenzene) has been investigated using both the supermolecular [second-order Moller–Plesset (MP2)] and perturbational (symmetry adapted perturbation theory) approaches. The geometry optimizations, harmonic vibrational frequencies, and the components of the binding energy were evaluated using fairly large basis sets (6-31+G* and aug-cc-pVDZ). The minimum energy structures obtained at the MP2/6-31+G* and MP2/aug-cc-pVDZ levels of theory indicate that the water dimer exhibits a π-type of interaction with ethene, benzene, and toluene and a σ-type of interaction with both fluorobenzene and p-difluorobenzene. This is demonstrated from the vibrational frequencies which are in good agreement with the experimentally determined numbers. Our calculations indicate that the nature and strength of the interaction of the donor water molecule (water dimer) with the π system has a significant bearing on the total binding energy of the complex. Apart from the interaction of the water dimer with the π system, we also show how this interaction influences the hydrogen bond characteristics of the water dimer by evaluating the hydrogen bond strengths.

Laser spectroscopy, i.e., resonant two-photon ionization (R2PI), IR/R2PI ion depletion and hole burning spectroscopy have been applied in an experimental study of heterogenous clusters consisting of fluorobenzene (FB) or p-difluorobenzene (pDFB), respectively, microsolvated by up to three methanol molecules. Their infrared ion depletion spectra were taken in the region of the OH and CH stretches of methanol. In these complexes the methanol molecules form subclusters, which are weakly hydrogen bonded to either the aromatic π-system (πOH) or to the fluorine substituent (σF) and a CH group (σCH). In FB⋅(MeOH)1, pDFB⋅(MeOH)1, pDFB⋅(MeOH)2 and one isomer of FB⋅(MeOH)2 the methanol subunits exclusively exhibit σF and σCH H-bonds. A further isomer of FB⋅(MeOH)2 exhibits a πOH type interaction. For FB⋅(MeOH)3 and pDFB⋅(MeOH)3 (1:3) complexes the methanol subcluster may take on either a chainlike or a ringlike conformation. In the chainlike isomer of FB⋅(MeOH)3 the methanol trimer interacts with the chromophore vi...

This combined experimental and computational study is aimed at elucidating the structure and reactivity of heterogeneous molecular clusters. We report results for the system para-chlorofluorobenzene/methanol (pClFB/MeOH). Particularly, three different van der Waals (vdW) isomers of the neutral (1:1) aggregate (π,σF,σCl) have been assigned by comparison of experimental infrared frequencies in the O–H and C–H stretch regions measured by IR/R2PI depletion spectroscopy with calculated frequencies at MP2/6-31+G(d) and B3LYP/6-31+G(d) level. The isomers are weakly hydrogen-bonded complexes with methanol’s OH group coordinated toward the aromatic π-electron cloud, the fluorine or the chlorine substituent, respectively. This assignment is corroborated by the UV and IR spectra of the corresponding monosubstituted benzene/methanol complexes. After resonant photoionization of pClFB⋅(MeOH)n, for n=1 besides vdW fragmentation, no chemical reactivity was observed for any isomer. The investigation of aggregates with n⩾5 indicated a substitution reaction taking place to produce chloroanisole+, emphasizing the importance of neutral precursor cluster size over cluster structure for intracluster ion–molecule reactions.

We have carried out a detailed investigation of the nature of the π-H interaction in the ethene–H2O, benzene–H2O, and benzene–(H2O)2 complexes using large basis sets (ranging from 6-31+G* to TZ2P++) and high levels of theory. The minimum geometries, and hence the vibrational frequencies, of all the complexes have been obtained at the second order Mo/ller–Plesset (MP2) level of theory. The binding energy of the ethene–H2O complex is only about 1 kcal/mol lower than that of the benzene–H2O complex. In the benzene–(H2O)2 complex, the interaction of benzene with the π-bonded water to that with the second water is nearly equivalent. In order to explain the above interesting facets of the interaction of water with benzene and ethene, the interaction energies were decomposed into the individual interaction energy components using the recently developed symmetry adapted perturbation theory (SAPT) program. The SAPT results indicate that the repulsive exchange energies play a crucial role in governing the energies ...

Recently, Brutschy and co-workers have reported the spectra of (substituted benzene)⋯(H2O)n systems. To investigate the possibility of these systems exhibiting a π–H kind of bonding interaction as observed in benzene⋯(H2O)n systems, we have carried out extensive ab initio calculations on different conformations of the fluorobenzene⋯(H2O) and p-difluorobenzene⋯(H2O) systems using various basis sets. Our results indicate that unlike the π interaction observed in benzene⋯(H2O)n, the O–H of the water molecule is involved in the formation of a six-membered ring system with the F–C–C–H of the aromatic ring. This six-membered ring which results from the formation of two H-bonds (water hydrogen and fluorine, water oxygen and benzene hydrogen), is extensively stabilized by electrostatic interactions. The strength of this σ-bonding interaction of water to fluorobenzene in C6H5F⋯H2O is nearly equal to the corresponding π-bonding interaction of water to benzene in C6H6⋯H2O. However the σ interaction of water to diflu...

Quantum mechanical ab initio calculations at the MP2/6-311++G** level of theory have been used to predict the binding energies and geometries of benzene−BX3 and ethene−BX3 (X = H, F, Cl) complexes. Single point calculations at a much higher level of correlation (MP4) and larger basis sets (6-311++G(2df,p) + diffuse(d,p)) have also been carried out. The calculations reveal interesting trends in their binding energies and geometries. The binding energies indicate that all of them are weakly bound van der Waals complexes with the exception of the C2H4−BH3 complex. While complexes involving BF3 are the weakest (binding energies) in cases of both ethene and benzene, there is a reversal in the relative order of the binding energies as one moves from ethene to benzene. Thus C6H6−BCl3 is more tightly bound than C6H6−BH3. The geometry exhibited by the lowest energy conformer in cases of complexes involving benzene is different from those involving ethene. In contrast to most weak van der Waals interactions involvi...

High level ab initio calculations have been performed on the benzene-HCl and benzene-HF systems using the second-order Mo/ller-Plesset perturbation theory. In contrast to existing theoretical studies, the calculated binding energies indicate that HCl binds more strongly to benzene than HF. This is in accordance with the limited experimental data available on these systems. An explanation has been forwarded for the above observation by performing a molecular orbital analysis of both C6H6⋯HF and C6H6⋯HCl. In the global minimum of C6H6⋯HF, HF lies inclined to the benzene ring with the hydrogen atom pointing either towards a benzene carbon or the center of carbon-carbon bond. In the C6H6⋯HCl complex, HCl is found to lie along the C6 axis of the benzene ring for smaller basis sets, but it also tends to lie inclined to the benzene ring for a very large basis set. The quantum mechanical probabilistic characterization of the structure of the C6H6⋯HCl complex provides a more realistic description of the experiment...

The geometries and vibrational frequencies of two conformers of pyruvic acid have been obtained at the ab initio second order Moller-Plesset level of theory using the 6–311++G∗∗ basis set. While the calculated geometries have been compared to the experimental microwave data, the vibrational frequencies have been assigned, using the experimental gas phase IR spectra of 13 isotopes of pyruvic acid by a recently developed scaling procedure (IRPROG). An attempt has been made to explain the stability of the eclipsed conformation over the staggered conformation of pyruvic acid by taking account of the molecular orbitals.

Ab initio calculations of proline and hydroxyproline zwitterions have been performed at the Hartree-Fock level using the 4-21++G basis set. The evaluated geometries have been compared to the corresponding X-ray parameters. The probable assignments for the experimental solid state vibrational spectra of proline and hydroxyproline based on the calculated ab initio frequencies and intensities were made.

The vibrational fingerprints of hydrogen-bonding associated with the adenine–thymine (A–T) Watson–Crick (WC) base pair have been identified in an infrared study of the A–T mimics 4-aminopyrimidine–1-methylthymine (4APM–1MT) and 4-aminopyrimidine–6-methyl-4-pyrimidinone (4APM–M4PMN) in the gas-phase. The IR vibrational spectra were measured via a double resonance scheme utilizing femtosecond multiphoton ionization. The changes in the molecular structure, anharmonic vibrational parameters, and the assignment of the observed vibrational spectra in the NH/CH stretch region were investigated by carrying out high-level theoretical calculations of the anharmonic spectra. The experimental observations and theoretical calculations indicate that the hydrogen bonds associated with WC base-pairing are relatively stronger than those associated with reverse WC (rWC) base pairing. This is manifested in a more pronounced red-shift of the H-bonded vibrational modes associated with the WC as compared with the rWC base-pairing. An analysis of the factors contributing to the anharmonicity of the vibrational modes associated with H-bonding reveals that the magnitude of the off-diagonal anharmonic coupling of the H-bonded –NH2 stretch and the –NH2 bend is much smaller in WC base-pairing than in the corresponding rWC base-pairing. The chemical and biological implications of these results, especially in the context of using vibrational spectroscopy as a tool for identifying the signatures of nucleotide base vibrations is addressed.

The conformations of the higher dicarboxylic acids HOOC(CH 2 ) n COOH, n = 1–4 , the hydroxymalonic acid have been studied at the HF/4-21G level of theory. The conformational characteristics of these acids have been elucidated through potential energy scans at this level. The vibrational frequencies of all the dicarboxylic acids have also been evaluated at this level. Calculations at the HF/6-31G ** level of theory were also carried out on malonic, hydroxymalonic and succinic acids. They have been assigned to the solid state Raman and IR spectra of the dicarboxylic acids. The potential energy distributions, Raman activities and IR intensities calculated at the levels indicated have been used as aids in making the assignments. The calculated frequencies have also been compared with the frequencies evaluated at the MP2/4-31G * level for oxalic acid.

The vibrational frequencies of cysteine and serine zwitterions are evaluated using ab initio methods at the 4–31G∗ level. The calculated frequencies along with the corresponding potential energy distributions are used to assign the IR and Raman spectra of the zwitterions of l -cysteine and d,l -serine. The calculated Raman activities, IR intensities along with the experimental Raman optical activities of these amino acids are used as aids in the assignments. The similarities and differences between the spectra of these amino acids are highlighted.

The ability to accurately predict the oxidation and reduction potentials of molecules is very useful in various fields and applications. Quantum mechanical calculations can be used to access this information, yet sometimes the usefulness of these calculations can be limited because of the computational requirements for large systems. Methodologies that yield strong linear correlations between calculations and experimental data have been reported, however the balance between accuracy and computational cost is always a major issue. In this work, linear correlations (with an R(2) value of up to 0.9990) between DFT-calculated HOMO/LUMO energies and 70 redox potentials from a series of 51 polycyclic aromatic hydrocarbons (obtained from the literature) are presented. The results are compared to previously reported linear correlations that were obtained with a more expensive computational methodology based on a Born-Haber thermodynamic cycle. It is shown in this article that similar or better correlations can be obtained with a simple and cheaper calculation.

Magnetic nanoparticles (MNPs) are of interest because their ability to convert electromagnetic energy into heat is of potential value in drug release, cancer therapy, and remote control of single cell functions. In the present paper, we focus our attention on TiO 2 -coated metallic magnetic core-shell nanoparticles (NPs) because of the high biocompatibility of TiO 2 . Our study of the electronic and spectral properties of these NPs indicates that the nature of the encapsulated metallic system has a profound influence on both their absorption and vibrational spectra. This observation is of interest because the efficacy of the energy transfer to the external environment of these systems is intricately related to the nature of coupling of the electronic levels to the vibrational modes.

Ab initio force fields for the vibrations of citric acid and citrate trianion in their ground electronic states have been determined at the Hartree—Fock level using the 4–21G basis set. The calculated geometries have been compared to the corresponding X-ray structures of citric acid and magnesium citrate, respectively. The calculated vibrational frequencies have been used to assign the experimental IR and Raman spectra of citric acid and sodium citrate. The calculated potential energy distribution, Raman activities and IR intensities have been used as aids in the assignment of the vibrational spectra of citric acid and sodium citrate.

We report the infrared spectrum of the 4-aminobenzimidazole-1-methylthymine (4ABI:1MT) heterodimer, detected by femtosecond multiphoton ionization. Based on calculations of both the harmonic and the anharmonic frequencies, the observed vibrational spectrum is assigned to a structure that mimics the Hoogsteen base pairing of adenine and thymine. A notable observation made in the course of this study is that there is a significant imbalance in the observed strengths of the H-bonds. While the N···H-N bond reveals a large red shift of700 cm(-1) for the NH stretch frequency, the N-H···O bond is characterized by only a 50 cm(-1) shift. The importance of this observation in the formation of Hoogsteen duplexes by thymine-based oligonucleotides is discussed.

Pseudorotation in the pyrrolidine molecule was studied by means of femtosecond degenerate four-wave mixing spectroscopy both in the gas cell at room temperature and under supersonic expansion. The experimental observations were reproduced by a fitted simulation based on a one-dimensional model for pseudorotation. Of the two conformers, axial and equatorial, the latter was found to be stabilized by about 29 +/- 10 cm(-1) relative to the former one. The barrier for pseudorotation was determined to be 220 +/- 20 cm(-1). In addition, quantum chemical calculations of the pseudorotational path of pyrrolidine were performed using the synchronous transit-guided quasi-Newton method at the MP2 and B3LYP levels of theory. Subsequent CCSD(T) calculations yield the energy preference of the equatorial conformer and the barrier for pseudorotation to be 17 and 284 cm(-1), respectively.

We report first-principles electronic structure calculations of hydrogen adsorption and saturation on ${M}_{13}$ $(M=\text{Sc},\text{Ti},\text{Zr})$ clusters of icosahedral $({I}_{h})$ and cuboctahedral $({O}_{h})$ symmetries. Hydrogen saturation of the ${I}_{h}$ metal clusters yields energetically stable ${M}_{13}{\text{H}}_{20}$ and ${M}_{13}{\text{H}}_{30}$ systems compared to ${M}_{13}{\text{H}}_{14}$ and ${M}_{13}{\text{H}}_{24}$ systems for ${O}_{h}$ clusters. In all these clusters, the hydrogen adsorption involves dissociative chemisorption of ${\text{H}}_{2}$ molecules. Upon initial hydrogenation, the dissociated hydrogen atoms lie above either the triangular or quadrangular face of the metal cluster. A further increase in hydrogen saturation leads to the formation of bridged hydrogen bond between adjacent metal atoms. The role of the unfilled $d$ orbitals in imparting stability to the hydrogenated clusters is explored by examining their density of states (DOS) near the Fermi level. It has been found that the inverse correlation between the $d$-band center and the chemisorption energies is valid only at low hydrogen concentrations. At higher hydrogen coverages, the trend is reversed. The results illustrate that at high adsorbate concentrations or surface coverage, the correlation of the chemisorption energies with the $d$-band center of the pure metal cluster or nanoparticle may not be realistic but one has to take into account the changes in the $d$-orbital DOS due to the presence of coadsorbed molecules. To obtain further insights into the initial steps involved in hydrogen adsorption and dissociation, the transition states and activation energies of the ${M}_{13}{\text{H}}_{2}$ system have been determined and found to conform with the empirical Br\o{}nsted-Evans-Polanyi relationship. A highly intense infrared band in the $1000\char21{}1500\text{ }{\text{cm}}^{\ensuremath{-}1}$ region, associated with the adsorbed hydrogens in these hydrogenated metal clusters, may be used to experimentally monitor hydrogen coverage.

Hydrogen undergoes dissociative chemisorption on small titanium clusters. How the electronic structure of the cluster changes as a function of the number of adsorbed hydrogen atoms is an important issue in nanocatalysis and hydrogen storage. In this paper, a detailed theoretical investigation of the structural, energetic, and electronic properties of the icosahedral Ti13 cluster is presented as a function of the number of adsorbed hydrogen atoms. The results show that hydrogen loaded Ti13H20 and Ti13H30 clusters are exceptionally stable and are characterized by hydrogen multicenter bonds. In Ti13H20, the dissociated hydrogen atoms are bound to each of the 20 triangular faces of Ti13, while in Ti13H30, they are bound to the 30 Ti-Ti edges of Ti13. Consequently, the chemisorption and desorption energies of the Ti13H20 (1.93 eV, 3.10 eV) are higher than that of Ti13H30 (1.13 eV, 1.95 eV). While increased hydrogen adsorption leads to an elongation of the Ti-Ti bonds, there is a concomitant increase in the electrostatic interaction between the dissociated hydrogen atoms and the Ti13 cluster. This enhanced interaction results from the participation of the subsurface titanium atom at higher hydrogen concentrations. Illustrative results of hydrogen saturation on the larger icosahedral Ti55 cluster are also discussed. The importance of these results on hydrogen saturated titanium clusters in elucidating the mechanism of hydrogen adsorption and desorption in titanium doped complex metal hydrides is discussed.

This work explores the nature of interaction and saturation of hydrogen molecules on small titanium clusters using ab initio calculations. Molecular dynamics simulations and ensuing charge density maps were used to gain insight into the key steps involved in dissociation of the hydrogen molecule on the metal clusters. The mechanistic insights gleaned from these simulations were subsequently utilized to obtain realistic models of the hydrogen saturated titanium clusters. It was found that the most stable hydrogen saturated titanium clusters involve hydrogen multicenter bonds. The observed peaks in the experimental mass and photoelectron spectra of hydrogen saturated titanium clusters are attributed to structures possessing hydrogen multicenter bonds. Hydrogen multicenter bonds are also ascribed to the origin of the broad shoulder in the vibrational spectra of hydrogen cycled Ti-doped NaAlH4 reported in a recent study.

We present the results of spectroscopic and photophysical investigations of 4-diethylaminopyridine (DEAP) and its 1 : 1 complexes with a number of protic solvents such as water and various alcohols of different acidity isolated under supersonic jet conditions. While a double resonance vibrational spectroscopic method was employed to investigate the size and geometrical structure of jet-cooled clusters, laser-induced fluorescence spectroscopy was used to examine the changes of photophysics induced by complexation of DEAP with solvent molecule(s). The results obtained from ab initio calculations enable the assignment of geometries and of the vibrational spectra of the clusters in the OH-stretch region. The comparison of the experimental and calculated vibrational spectra indicates that the solvent molecule is hydrogen-bonded to the pyridine nitrogen atom. Dual luminescence is observed only for the complexes with alcohols of relatively strong acidity.

The observed performances of carbon nanotube field effect transistors are examined using first-principles quantum transport calculations. We focus on the nature and role of the electrical contact of Au and Pd electrodes to open-ended semiconducting nanotubes, allowing the chemical contact at the surface to fully develop through large-scale relaxation of the contacting atomic configuration. We present the first direct numerical evidence of Pd contacts exhibiting perfect transparency for hole injection as opposed to that of Au contacts. Their respective Schottky barrier heights, on the other hand, turn out to be fairly similar for realistic contact models. These findings are in general agreement with experimental data reported to date, and show that a Schottky contact is not merely a passive ohmic contact but actively influences the device I-V behavior., Submitted to PRL

Interactions involving aromatic rings are important in molecular/biomolecular assembly and engineering. As a consequence, there have been a number of investigations on dimers involving benzene or other substituted pi systems. In this Feature Article, we examine the relevance of the magnitudes of their attractive and repulsive interaction energy components in governing the geometries of several pi-pi systems. The geometries and the associated binding energies were evaluated at the complete basis set (CBS) limit of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using a least biased scheme for the given data set. The results for the benzene dimer indicate that the floppy T-shaped structure (center-to-center distance: 4.96 A, with an axial benzene off-centered above the facial benzene) is isoenergetic in zero-point-energy (ZPE) corrected binding energy (D0) to the displaced-stacked structure (vertical interplanar distance: 3.54 A). However, the T-shaped structure is likely to be slightly more stable (D0 approximately equal to 2.4-2.5 kcal/mol) if quadruple excitations are included in the coupled cluster calculations. The presence of substituents on the aromatic ring, irrespective of their electron withdrawing or donating nature, leads to an increase in the binding energy, and the displaced-stacked conformations are more stabilized than the T-shaped conformers. This explains the wide prevalence of displaced stacked structures in organic crystals. Despite that the dispersion energy is dominating, the substituent as well as the conformational effects are correlated to the electrostatic interaction. This electrostatic origin implies that the substituent effect would be reduced in polar solution, but important in apolar media, in particular, for assembling processes.

The design of cesium-selective ionophores must include the nature of cesium-water interactions. The authors have carried out extensive ab initio and density functional theory calculations of hydrated cesium cations to obtain reasonably accurate energetics, thermodynamic quantities, and IR spectra. An extensive search was made to find the most stable structures. Since water...water interactions are important in the aqua-Cs+ clusters, the authors investigated the vibrational frequency shifts as a function of the number of water molecules and the frequency characteristics with and without the presence of outer-shell water molecules. The predicted vibrational frequencies were then compared with the infrared photodissociation spectra of argon-tagged hydrated cesium cluster ions. This comparison allowed the identification of specific hydrogen-bonding structures present in the experimental spectra.

Thermogalvanic cells, also known as thermoelectrochemical cells or simply as thermocells, have recently attracted a lot of attention because of their immense potential in converting low-grade thermal energy to electricity. The thermal temperature coefficient of electrode potential (α) in a thermogalvanic cell is directly proportional to the change in entropy (ΔS) of the redox reaction in the cell through the relation (α = ∂E/∂T = ΔS/nF), where E is the cell potential, T the temperature, n the number of electrons involved in the reaction, and F the Faraday’s constant. Although the nature of effects are different, α is often referred to as the Seebeck coefficient. In an ideal thermogalvanic cell, one therefore prefers to employ a redox couple exhibiting the largest α. Therefore, in the current study we discuss an alternate method to enhance ΔS for the electron transfer process. Thus, by coupling a redox process to solution phase complexation, we show that there is marked increase in both the change in entropy and the resulting α. While the change in entropy was calculated using quantum-chemical methods, α was experimentally measured for a Cu/Cu2+ thermogalvanic cell. The results indicate that a complexation of the Cu2+ species with a dissolved polymer, such as poly(acrylic acid) (PAA) or ethylenediaminetetraacetic acid (EDTA), dramatically improve α by up to 75%. We believe, that this novel approach to enhance α, would prove to be useful in the development of thermodynamically more efficient thermogalvanic cells.

Hydrogen bonds (H-bonds) are relatively weak and result from non- covalent interactions. Despite their relatively low strength compared to other bonds of biochemical relevance, they play a vital role in determining the structure and function of biological molecules owing to their directionality and cooperativeness. This has led to an intense effort in harnessing the properties of these hydrogen bonds in developing organic electronic devices. Though a large number of theoretical investigations have devoted their attention to the structural andenergeticcharacteristicsofhydrogenbonds,therearerelativelyfewstudieson theelectronictransportcharacteristicsofhydrogenbonds.Inthisworkweevaluate the electrical conductance of a few model systems exhibiting the biologically important hydrogen bonds (N-H O, O-H O and N-H N). We find that the calculated conductance can be correlated to the magnitude of the polarisabilities of the atoms involved in the formation of the hydrogen bonds. The implications of the current work in understanding electron transfer in biological systems is highlighted.Wealsoaddresstheutilityofourworkinthedesignanddevelopment of novel sensors and electronic devices based on the formation of weak hydrogen bonds.

Electrophilic aromatic substitution reactions, which are highly exemplified by the widely used Friedel-Craft's reaction, have been extensively studied using theoretical and experimental techniques. A number of elegant mechanisms have been proposed for the Friedel-Craft's reaction till date. In all the proposed mechanisms, the role of the Lewis acid has been limited to the generation of the electrophile, which subsequently attacks the aromatic system to form either a π or a σ complex. A recent experimental report on the reaction of CO with benzene in zeolite catalysts intrigued us because the presence or absence of AlCl3 was found to govern the reaction product. These clearly indicated that AlCl3 has an additional role in the reaction. We probed this role theoretically by performing high-level ab initio calculations on two model systems C6H6−BCl3 and C6H6−AlCl3. Our results clearly indicate that one of the benzene carbon tends to become highly nucleophilic, thereby facilitating an attack by an incipient el...

Examined in this paper is the role of the metal electrode influencing the structure and electronic properties of semiconducting carbon nanotubes near the interface at low bias. Specifically, we present quantum-chemical calculations of finite sections of a (8,0) semiconducting single wall nanotube contacted with gold and palladium clusters. The calculations at the density functional level of theory, which included full geometry optimizations, indicate the formation of bonds between the metal atoms of the electrode and the carbon atoms of the nanotube. The local work function of the metal electrode can be expected to exhibit significant variations as a result of this bond formation. Compared to the gold-contacted nanotubes, the palladium-contacted nanotubes have a small but interesting increase in both length and diameter. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the gold-contacted nanotube are shown localized at the edges. In contrast, the HOMO and LUMO of the palladium-contacted nanotube are extended over the entire nanotube and the metal cluster contacted to it, providing thereby a better conduction path in the contact region of the electrode and the nanotube. The involvement of the highly directional d orbitals in the interactions involving the palladium cluster leads to an enhanced pi electron density in the nanotube. This enhanced pi electron density is synonymous with an improved electron transmission.

Among the several weak intermolecular interactions pervading chemistry and biology, the NH-pi interaction is one of the most widely known. Nevertheless its weak nature makes it one of the most poorly understood and characterized interactions. The present study details the results obtained on gas-phase complexes of ammonia with various substituted pi systems using both laser vibrational spectroscopy and ab initio calculations. The spectroscopic measurements carried out by applying one-color resonant two-photon ionization (R2PI) and IR-vibrational predissociation spectroscopy in the region of the NH stretches yield the first experimental NH stretching shifts of ammonia upon its interaction with various kinds of pi-systems. The experiments were complemented by ab initio calculations and energy decompositions, carried out at the second-order Møller-Plesset (MP2) level of theory. The observed complexes show characteristic vibrational spectra which are very similar to the calculated ones, thereby allowing an in-depth analysis of the interaction forces and energies. The interaction energy of the conformers responsible for the observed vibrational spectra has the maximum contribution from dispersion energies. This implies that polarizabilities of the pi-electron systems play a very important role in governing the nature and geometry of the NH-pi interaction. The larger polarizability of ammonia as compared to water and the tendency to maximize the dispersion energy implies that the characteristics of the NH-pi interactions are markedly different from that of the corresponding OH-pi interactions.

Using molecular-orbital analysis, we have elucidated the quantum-chemical origin of the intriguing phenomena in sequential hydration energies of the gold cation, which is known to be the most conspicuous among all transition metals. The hydration energy of Au+ with the second water molecule is found to be much larger than that with the first water molecule. Owing to the large relativistic effect of gold (i.e., significant lowering of the 6s orbital energy and significant raising of the 5d orbital energy), the highest occupied molecular orbital of the hydrated gold cation has a large portion of the 6s orbital. As the electron density of the 6s orbital populates in a large outer spherical shell far off the gold nucleus, the p orbitals (or sp hybridized lone-pair orbitals) of the water molecules are able to overlap with the outer part of the 6s orbital in the dihydrated gold cation, resulting in the unusual skewed overlap of p-6s-p orbitals (not the atom-to-atom bond overlap). No previous molecular-orbital analysis has reported this peculiar skewed orbitals overlap. Since this skewed orbitals overlap is saturated with two water molecules, this property is responsible for the low coordination number of the gold ion.

The edge-to-face interactions for either axially or facially substituted benzenes are investigated by using ab initio calculations. The predicted maximum energy difference between substituted and unsubstituted systems is approximately 0.7 kcal/mol (approximately 1.2 kcal/mol if substituents are on both axially and facially substituted positions). In the case of axially substituted aromatic systems, the electron density at the para position is an important stabilizing factor, and thus the stabilization/destabilization by substitution is highly correlated to the electrostatic energy. This results in its subsequent correlation with the polarization and charge transfer. Thus, the stabilization/destabilization by substitution is represented by the sum of electrostatic energy and induction energy. On the other hand, the facially substituted aromatic system depends on not only the electron-donating ability responsible for the electrostatic energy but also the dispersion interaction and exchange repulsion. Although the dispersion energy is the most dominating interaction in both axial and facial substitutions, it is almost canceled by the exchange repulsion in the axial substitution, whereas in the facial substitution, together with the exchange repulsion it augments the electrostatic energy. The systems with electron-accepting substituents (NO2, CN, Br, Cl, F) favor the axial substituent conformation, while those with electron-donating substituents (NH2, CH3, OH) favor the facial substituent conformation. The interactions for the T-shape complex systems of an aromatic ring with other counterpart such as H2, H2O, HCl, and HF are also studied.

Publisher Summary This chapter discusses how the insights obtained from theoretical investigations of various cluster systems have enabled a researcher to predict structures and properties of novel functional molecular systems. Clusters are self-assembled structures comprised of a number of monomers under the given condition. Apart from aiding the development of novel materials, clusters are very useful for understanding the intrinsic and fundamental nature of molecular recognition and self-assembling phenomena. This is amply illustrated in a number of publications on a wide variety of atomic and molecular clusters, ranging from H-bonded clusters, p-system-containing clusters, and metal clusters. These investigations not only provide pertinent information useful for nanomaterial design but also highlight some of the important similarities and differences in their physical characteristics. These characteristics include structures, magnitudes of both attractive and repulsive interaction energies, vibrational frequencies, and charge redistributions. Additionally, one also obtains an insight into the contributions of cooperative and competitive forces, both of which govern self-assembly and molecular recognition.

This chapter discusses theoretical approaches to the design of functional nanomaterials. A theoretical description of nanomaterials that belongs to the mesoscopic phase is fraught with a number of problems because neither quantum–chemical methods used to investigate the microscopic phase nor solid-state physics methods used to investigate the macroscopic phase can adequately describe all the desired properties. A judicious combination of both these methods apart from providing a detailed insight of the properties of these nanomaterials also aids the de novo design of novel molecular systems and functional materials. Another area of interest is molecular recognition, wherein quantum chemical calculations aid the design of microscopic chemical/biochemical sensors/monitors such as DNA chips. This chapter examines the ways in which an effective combination of diverse theoretical methods ranging from traditional ab initio , density functional, tight binding, Monte Carlo to molecular dynamics simulations, have helped elucidate the nature of intermolecular interactions in a large number of widely disparate molecular complexes (aqueous and metal clusters, biomolecules), and have also aided the design of novel nanomaterials (ionophores, receptors, endo/exohedral fullerenes, fullerides, nanotori, nanotubes, nanowires, and molecular devices).

The highly stereospecific and regiospecific recognition of alpha-amino acids exhibited by a novel Co(III) metal complex embodied in the experimental work (Nature 1999, 401, 254) is rationalized from the energetics and structural characteristics with the use of density functional calculations. The steric repulsion between the chiral center of the receptor [Co(III) complex] and alanine has been a cause for the discrimination of complex stabilities. The energies evaluated for all possible alanine binding modes clearly reveal regiospecificity. Our main emphasis is laid on the base-catalyzed epimerization reaction that drives the stereospecific recognition to near completion. The conducted tour mechanism is found to be the most likely candidate. A similar role by the equivalent Zn(II) complex is found.

We use first principles calculations to investigate the structure and electronic properties of ultrathin silver (Ag) nanowires self-synthesized in organic calix[4]hydroquinone (CHQ) nanotubes. The insulating CHQ nanotubes get transformed to semiconducting calix[4]diquinone-dihydroquinone (CQHQ) tubes in the presence of Ag. These encapsulated nanowires have linear crystalline structure. The electron density around the Fermi level is localized on the Ag nanowire. This indicates that the organic tubes act as shields between Ag nanowires, and the quantum confinement is possible in the encapsulated Ag nanowires like in quantum dots.

Ab initio calculations have been employed to investigate the peculiar change in magnetic property (from diamagnetic to paramagnetic) of the dianionic C60-dimer phase in a rapidly cooled AC60 samples ( A: alkali metal). We first note that the triplet state of (C60)-22 which was never considered previously is nearly degenerate with the singlet state, and the transition barrier between the two states is reasonably small. This explains the susceptibility increase with an increase in temperature and the magnetic phase transition in the process of the dimer to monomer phase transition.

A new strategy for reversible hydrogen storage based on the properties of hydrogen multicenter bonds is proposed. This is demonstrated by carrying out ab initio calculations of hydrogen saturation of titanium and bimetallic titanium-aluminum nanoclusters. Hydrogen saturation leads to the formation of exceptionally and energetically stable hydrogen multicenter bonds. The stabilization results from sharing of the hydrogen atom electron density with the frontier orbitals of the metal cluster. The strength of the hydrogen multicenter bonds can be modulated either by varying the degree of hydrogen loading or by suitable alloying. Mode-specific infrared excitation of the vibrational modes associated with the multicenter hydrogen bonds can release the adsorbed hydrogen, thereby enabling efficient reversible hydrogen storage. The possible formation of hydrogen multicenter bonds involving titanium atoms and its implication to hydrogen adsorption/desorption kinetics in hydrogen cycled Ti-doped NaAlH(4) is also discussed.

In an effort to examine the intricacies of electronic nanodevices, we present an atomistic description of the electronic transport properties of an isolated benzene molecule. We have carried out ab initio calculations to understand the modulation of the molecular orbitals (MOs) and their energy spectra under the external electric field, and conducting behavior of the benzene molecule. Our study shows that with an increase in the applied electric field, the energy of the third lowest unoccupied molecular orbital (LUMO) of benzene decreases, while the first and second LUMO energies are not affected. Above a certain threshold of the external electric field, the third LUMO is lowered below the original LUMO and becomes the real LUMO. Since the transport through a molecule is to a large extent mediated by the molecular orbitals, the change in MOs can lead to a dramatic increase in the current passing through the benzene molecule. Thus, in the course of this study, we show that the modulation of the molecular orbitals in the presence of a tuning parameter(s) such as the external electric field can play important roles in the operation of molecular devices. We believe that this understanding would be helpful in the design of electronic nanodevices.

Electron-bound water clusters [e(-)(H(2)O)(n)] show very strong peaks in mass spectra for n=2, 6, 7, and (11), which are called magic numbers. The origin of the magic numbers has been an enigma for the last two decades. Although the magic numbers have often been conjectured to arise from the intrinsic properties of electron-bound water clusters, we attributed them not to their intrinsic properties but to the particularly weak stability of the corresponding neutral water clusters (H(2)O)(n=2,6,7, and (11)). As the cluster size increases; this nonsmooth characteristic feature in stability of neutral water clusters is contrasted to the smooth increase in stability of e(-)-water clusters. As the magic number clusters have significant positive adiabatic electron affinities, their abundant distributions in atmosphere could play a significant role in atmospheric thermodynamics.

The present report details the results of a high-level theoretical investigation of benzene−AlX3 and ethene−AlX3 (X = H, F, Cl) interactions. The binding energies, preferred modes of interaction of AlX3 with benzene and ethene, and vibrational frequencies for these complexes have been evaluated at the MP2 level using basis sets ranging from the 6-31+G* to the much larger (6-311++G(2df,p) + diffuse(d,p)). In the lowest energy conformers of the benzene complexes, the Al atom is directly placed over one of the benzene carbons, while in the ethene complexes, the Al atom lies above the center of the π bond. The binding energies of both the benzene and ethene complexes of AlX3 are dominated by electrostatic contributions, which is in contrast to the dominance of the electron correlation energy in the benzene−BX3 complexes. A very sharp increase in the negative charge of the benzene carbon closest to the Al atom in the lowest energy conformers of the benzene complexes from −0.2 to −0.4 au points to an important ...

The vibrational frequencies of two conformations of proline and hydroxyproline in the non-ionized form have been evaluated using the ab initio method at the HF/4-21G level. The barrier heights of the rotation of the carboxy and hydroxy hydrogen atoms have been evaluated at the HF/4-21G level. The calculated frequencies are assigned to the experimental vibrational spectra of proline and hydroxyproline.

The vibrational frequencies of three conformations of cysteine and serine in the non-ionized form have been evaluated using ab initio methods at the 4-31G ∗ level. The calculated frequencies along with the corresponding potential energy distributions were used to assign the IR spectra of the methyl ester, hydrochloride and zwitterion of cysteine and serine. It was found that the v (C β X) frequency is dependent on the value of X 1 [CC α C β X] torsional angle. The conformational dependence of some of the frequencies have been highlighted.