Photoionization-induced water migration in the hydrated trans-formanilide cluster cation revealed by gas-phase spectroscopy and ab initio molecular dynamics simulation

Photoionization-induced water migration in the trans-formanilide-water 1:1 cluster, FA-(H(2)O)(1), has been investigated by using IR-dip spectroscopy, quantum chemical calculations, and ab initio molecular dynamics simulations. In the S(0) state, FA-(H(2)O)(1) has two structural isomers, FA(NH)-(H(2)O)(1) and FA(CO)-(H(2)O)(1), where a water molecule is hydrogen-bonded (H-bonded) to the NH group and the CO group, respectively. In addition, the S(1)-S(0) origin transition of FA(CO)-(H(2)O)(2), where a water dimer is H-bonded to the CO group, was observed only in the [FA-(H(2)O)(1)](+) mass channel, indicating that one of the water molecules evaporates completely in the D(0) state. These results are consistent with a previous report [Robertson, E. G. Chem. Phys. Lett., 2000, 325, 299]. In the D(0) state, however, [FA-(H(2)O)(1)](+) produced by photoionization via the S(1)-S(0) origin transitions of FA(NH)-(H(2)O)(1) and FA(CO)-(H(2)O)(1) shows essentially the same IR spectra. Compared with the theoretical calculations, [FA-(H(2)O)(1)](+) can be assigned to [FA(NH)-(H(2)O)(1)](+). This means that the water molecule in [FA-(H(2)O)(1)](+) migrates from the CO group to the NH group when [FA-(H(2)O)(1)](+) is produced by photoionization of FA(CO)-(H(2)O)(1). [FA-(H(2)O)(1)](+) produced by photoionization of FA(CO)-(H(2)O)(2) also shows the IR spectrum corresponding to [FA(NH)-(H(2)O)(1)](+). In this case, the water migration from the CO group to the NH group occurs with the evaporation of a water molecule. Ab initio molecular dynamics simulations revealed the water migration pathway in [FA-(H(2)O)(1)](+). The calculations of classical electrostatic interactions show that charge-dipole interaction between FA(+) and H(2)O induces an initial structural change in [FA-(H(2)O)(1)](+). An exchange repulsion between the lone pairs of the CO group and H(2)O in [FA-(H(2)O)(1)](+) also affects the initial direction of the water migration. These two factors play important roles in determining the initial water migration pathway.     

A direct ab initio dynamics study of the water-assisted tautomerization of formamide

Direct ab initio dynamics calculations based on a canonical variational transition-state theory with several multidimensional semiclassical tunneling approximations were carried out to obtain rate constants for the water-assisted tautomerization of formamide. The accuracy of the density functionals, namely, B-LYP, B3-LYP, and BH&H-LYP, were examined. We found that the BH&H-LYP method yields the most accurate transition-state properties when comparing it to ab initio MP2 and QCISD results, whereas B-LYP and B3-LYP methods predict barrier heights too low. Reaction path information was calculated at both the MP2 and nonlocal hybrid BH&H-LYP levels using the 6–31G(d,p) basis set. At the BH&H-LYP level, we found that the zero-point energy motion lowers the barrier to tautomerization in the formamide-water complex by 3.6 kcal/mol. When tunneling is considered, the activation energy at the BH&H-LYP level at 300 K is 17.1 kcal/mol. This is 3.4 kcal/mol below the zero-point-corrected barrier and 7.0 kcal/mol below the classical barrier. Excellent agreement between BH&H-LYP and MP2 rate constants further supports the use of BH&H-LYP for rate calculations of large systems. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63: 861–874, 1997     

Calculated physical properties of a water molecule in an ice-Like cluster

Some properties of a H₂O molecule surrounded by the four nearest neighbours arranged as in the ice I geometry have been calculated within a SCF scheme in terms of an extended STO's basis. The effect of the outer molecules is treated as a coulombic perturbation. The different possible geometric configurations of the perturbators have been taken into account. Comparisons are made with the experimental changes of some physical properties of water in passing from vapor to condensed phase.

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Zusammenfassung Es werden einige Eigenschaften des Wassermoleküls, das von seinen vier nächsten Nachbarn in Eis-I-Geometrie umgeben ist, mit Hilfe eines SCF-Schemas mit erweiterter STO-Basis berechnet. Dabei wird der Effekt der äußeren Moleküle als Coulombstörung behandelt. Die verschiedenen möglichen geometrischen Konfigurationen der Störmoleküle sind in Betracht gezogen worden. Die Rechenergebnisse werden mit den experimentellen Änderungen einiger physikalischer Eigenschaften des Wassers beim Übergang von der Gasphase zur kondensierten Phase verglichen.

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Work performed with the C.N.R. financial aid.     

单笼形水分子簇中心水分子对类型关系

随机产生单笼形水分子簇(H2O)n(n=8~36),经分类统计后发现,在笼形水分子簇中,其1221,1212,2121和2112四类氢键的个数与水分子和氢键总数之间有定量关系,且1212类氢键的个数与2121类的氢键始终相等.如果笼形水分子簇中某一类氢键数已知,则它的其余三类氢键的个数也随即确定.     

Mode-dependent enhancement of photodissociation and photoionization in a seven atom molecule

We report the first experimental demonstration of vibrational mode-dependent enhancement in photodissociation and photoionization of a seven atom molecule, methylamine (CH(3)NH(2)). The fundamental C-H stretches and the overtones or combinations of CH(3) bends were prepared via stimulated Raman excitation (SRE) prior to their 243.135 nm one-photon dissociation or two-photon ionization. The photodissociation or photoionization of the vibrationally excited molecules was achieved via 10 ns delayed or temporally overlapping SRE and UV pulses, respectively. It is shown that bending modes are more effective than stretches in promoting photodissociation and photoionization, since their UV excitation is favored by larger Franck Condon factors. This behavior provides clear evidence for vibrational mode-dependence in a relatively large molecule with a torsional degree of freedom, indicating that these modes survive intramolecular vibrational redistribution on a time scale considerably longer than hitherto inferred from previous studies.     

Entropy-driven rearrangement of the water network at the hydrated amide group of the trans-formanilide-water cluster in the gas phase

Photoionization-induced rearrangement of the water network in the trans-formanilide 1:4 cluster, FA-(H(2)O)(4), has been investigated by using IR-photodissociation spectroscopy and quantum chemical calculations. The IR spectrum of FA-(H(2)O)(4) in the S(0) state shows that the observed cluster has a cyclic hydrogen-bonded structure where the CO group and the NH group of FA are bridged with four water molecules, consistent with the reported structure [E. G. Robertson, Chem. Phys. Lett., 2000, 325, 299]. However, the corresponding cyclic hydrogen-bonded structure in the D(0) state of [FA-(H(2)O)(4)](+) is a minor product arising from photoionization via the S(1)-S(0) origin of FA-(H(2)O)(4). The dominant product has an extended H-bonded structure, where the intermolecular hydrogen bond between the hydrogen of the OH group of a water molecule and the CO group is dissociated. This is the first observation of a photoionization-induced rearrangement of the water network in [FA-(H(2)O)(4)](+). Through DFT calculations, we conclude that the rearrangement occurs due to entropic effects.     

Density functional theory study of the oxidation of methanol to formaldehyde on a hydrated vanadia cluster

Density functional theory was used to study the mechanism for the oxidation of methanol to formaldehyde. A vanadium oxide cluster O?V(OH)₃ has been utilized to represent the catalytic system under hydrated conditions, i.e., in the presence of V? OH hydroxyl groups. Two types of methoxy‐intermediates have been considered: a penta‐coordinate methoxy‐intermediate (OH)₄V(OCH₃) and a tetrahedral methoxy‐intermediate (OH)₂VO(OCH₃)(H₂O). The most plausible reaction pathway corresponds to the process involving first the formation of the tetrahedral methoxide, and a subsequent rate‐limiting step where hydrogen is transferred from the methoxy groups toward the oxygen atom of the vanadyl V?O site. The reaction mechanism is a typical two‐state reactivity process due to a change of the multiplicity (reactive singlet → product triplet) along the reaction coordinate accompanied by a reduction of the vanadium center from V^V (d⁰) to V^III (d²). Minimum energy crossing points were localized and possible spin inversion processes are discussed by means of the intrinsic reaction coordinate approach to find the most favorable reaction pathways. The hydration effect is found to be mainly the destabilization of the methoxy intermediates. An alternative reaction pathway with a lower apparent barrier is presented. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Solvent migration from the C- to the N-terminus of amino acid in photoionization of phenylglycine-water complex

Photo-oxidation of amino acids is known to generate reactive protein radicals that lead to lethal disorders. We investigated photoionization of hydrated phenylglycine complexes in the gas phase and found that the excess internal energy from photoionization drives decarboxylation in competition with dehydration. We also found that, in decarboxylation, the solvent migrates a large distance from the C terminus of the neutral amino acid to the N terminus of the newly formed radical cation upon ionization, prior to the departure of the carboxyl group. It is noted that a solvent does not just act as a passive medium bound to the solute molecule but actively pursues its own course of action upon external perturbation that changes its chemical environment.     

Long-range radical cation migration in DNA: investigation of the mechanism

During the past decade, long-range radical cation migration in DNA has been an area of extensive experimental and theoretical examination. The motivations for the vigorous investigation of this topic are its potential to yield a deeper understanding of the processes that cause oxidative damage of genomic DNA and the potential for use of DNA architectures in molecular electronics. This investigation has revealed the mechanisms of charge transport and the limitations of DNA as a functional element in devices. In this article we discuss various aspects of the radical cation migration process and present the plausible mechanism by which this process occurs.     

Study of the bands attributable to crystallization water in hydrated metal acetates

A comparison of spectra recorded on hydrated, deuterated and anhydrous metal acetates enables the absorptions between 900 and 700 cm⁻¹ and between 580 and 500 cm⁻¹ in hydrated salts to be assigned to librational modes of crystallization water. Bands with wavenumbers lower than 450 cm⁻¹ were assigned to metal—oxygen vibrations. The data reported can be a basis for the study of the dehydration of the salts examined by i.r. spectrometry.     

Micro-gasometric determination of water in hydrated salts

Summary The method ofElitsur for gasometric determination of water in hydrated salts by the liberation of hydrogen resulting from the interaction between calcium hydride and hydrated salt in pyridine medium has been made applicable to micro scale by the use of suitable apparatus and procedure.Determinations of water of hydration are reproducible within 0.3% H₂O of the theory.

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Zusammenfassung Das gasvolumetrische Verfahren vonElitsur, das auf der Entbindung von Wasserstoff beim Erhitzen der wasserhältigen Substanz mit Pyridin und Calciumhydrid beruht, wurde durch Wahl eines geeigneten Apparates und eines Vorgehens zur Entfernung von Feuchtigkeitsspuren aus Apparat und Reagensmischung unmittelbar vor Beginn der Bestimmung für die Ausführung im Mikromaßstab geeignet gemacht. Bestimmungen von Kristallwasser können innerhalb 0,3% H₂O vom Sollwert ausgeführt werden.

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Résumé L'emploi d'un appareil et d'une technique convenables a permis d'étendre à l' échelle microanalytique la méthode deElitsur pour le dosage gazométrique de l'eau dans les sels hydratés par dégagement d' hydrogène résultant de leur réaction sur l'hydrure de calcium en milieu pyridinique.Les résultats obtenus sont reproductibles et diffèrent de moins de 0,3% H₂O des résultats théoriques.

     

Stationary point structure and energetics: Density functional study including solvent effects on the tautomerization of formamide and 2-pyridone

Solvent effects on the thermodynamics and kinetics of some tautomerization reactions, chosen as the most representative of this wide class of reactions, are analyzed. Solvent effects have been modeled by the self-consistent reaction field approach that we have implemented in the ADF package. We investigated the structure and energetics of the saddle points for the formamide/formamidinic acid and 2-pyridone/2-hydroxypyridine tautomerizations. Our results, carried out both at local and gradient corrected levels, are in good agreement with previous post-Hartree–Fock computations in predicting the structure and the energy of the investigated saddle points. On the other hand, our computations show that solvent effects play a relevant role on the energetics of the reactions. In particular, the interconversion of 2-hydroxypyridine into 2-pyridone is sensibly favored in aqueous solution, being that the latter tautomers are stabilized by solvent interactions. This latter result is in agreement with experimental findings. © 1995 John Wiley & Sons, Inc.     

Formation of silver nanoparticles in formamide:water mixtures: a radiolytic study

The pulse radiolysis of FA and FA:water solutions was studied in the absence and presence of redox indicator 1,1′-dimethyl-4,4′-bipyridinium dichloride (methyl viologen, MV²⁺). The experiments performed in the presence of MV²⁺ have provided strong support to the idea that the first species obtained from the reaction of e_sol⁻ and ^•OH with FA produces radicals that show reactivity towards the MV²⁺. Both the radicals on reaction with MV²⁺ results in the appearance of the well-known intense blue MV^•+ radical absorption signal (λ_max = 395 nm, λ_max = 605 nm). The intermediate radicals formed during radiolysis were used to generate silver nanoparticles.     

Topological analysis of the charge density response of a Ni4 cluster to a probe H2 molecule

Local density self-consistent field (SCF) discrete variationalX calculations are performed on a Ni₄ tetrahedron interacting with a probe H₂ molecule in special geometries. Optimized basis functions generated from the spherically averaged SCF potential are used. Topological charge-density analyses and binding energy calculations are used to study a portion of the energy surface for the approach of the H₂ molecule toward the Ni₄ tetrahedron. The effect of the H₂ molecule on Ni-Ni, Ni-H bonds and changes in the H-H covalent bond are investigated with the help of the field and various data at its critical points. The qualitative relationship between these data and the calculated binding energies is exploited.     

Size-specific reactions of copper cluster ions with a methanol molecule

Chemisorption of a methanol molecule onto a size-selected copper cluster ion, Cu(n)+ (n = 2-10), and subsequent reactions were investigated in a gas-beam geometry at a collision energy less than 2 eV in an apparatus based on a tandem-type mass spectrometer. Mass spectra of the product ions show that the following two reactions occur after chemisorption: dominant formation of Cu(n-1)+(H)(OH) (H(OH) formation) in the size range of 4-5 and that of Cu(n)O+ (demethanation) in the size range of 6-8 in addition to only chemisorption in the size range larger than 9. Absolute cross sections for the chemisorption, the H(OH) formation, and the demethanation processes were measured as functions of cluster size and collision energy. Optimized structures of bare copper cluster ions, reaction intermediates, and products were calculated by use of a hybrid method (B3LYP) consisting of the molecular orbital and the density functional methods. The origin of the size-dependent reactivity was explained as the structural change of cluster, two-dimensional to three-dimensional structures.     

Cobalt-phosphate complexes catalyze the photoelectrochemical water oxidation of BiVO4 electrodes

BiVO(4) semiconductor electrodes were coupled with cobalt-phosphate complexes (CoPi) to enhance the photoelectrochemical (PEC) performance for water oxidation reaction. CoPi was deposited on a 550 nm-thick BiVO(4) film via electrodeposition (ED) and photodeposition (PD) methods for comparison of their effects. The CoPi on BiVO(4) exhibited Co?:?P atomic ratios of approximately 1?:?7 for the electrodeposited sample and approximately 1?:?18 for the photodeposited sample, and Co(2+) and Co(3+) co-existed in both samples. Optimized CoPi ED resulted in a CoPi overlayer of approximately 850 nm thick, which showed an electrochromic-like behavior that was likely due to limited access of phosphate into BiVO(4) across the CoPi layer. Optimized CoPi PD, however, had very thin and rather uniform CoPi dispersion and did not show electrochromic-like behavior. Despite the lesser amount of CoPi, the PEC performance of BiVO(4)/CoPi (PD) was comparable to that of BiVO(4)/CoPi (ED). Real-time measurements of the headspace molecular oxygen that evolved from water oxidation indicated that CoPi enhances O(2) production and photocurrent generation at BiVO(4) by a factor of around 15 and a maximum of 20, respectively, at 0.576 V(SCE) (equivalent to 1.23 V(RHE)) under air mass 1.5 irradiation (400 mW cm(-2)). Prolonged irradiation of BiVO(4)/CoPi (ED) resulted in a reduced Co?:?P ratio to 1?:?1.77 without changing the mixed valency of Co(II/III). This finding indicates that incorporation of phosphate into the CoPi was kinetically slower than water oxidation. The primary role of CoPi has been suggested as a hole-conducting electrocatalyst making the photogenerated electrons more mobile and, consequently, increasing conductivity and boosting the PEC water oxidation performance of BiVO(4).     

The influence of water molecule coordination to a metal ion on water hydrogen bonds

The geometry of hydrogen bonds in the crystal structures from the Cambridge Structural Database and calculated data show that water coordination to a metal ion has a remarkable influence on hydrogen bonds. The calculated energies of hydrogen bonds of coordinated water are much stronger, even if the aqua complex is neutral.