On the ion‐pair dissociation mechanisms in the small NaCl·(H2O)6 cluster: A perspective from reaction path search calculations

We performed reaction path search calculations for the NaCl·(H₂O)₆ cluster using the global reaction route mapping (GRRM) code to understand the atomic‐level mechanisms of the NaCl → Na⁺ + Cl⁻ ionic dissociation induced by water solvents. Low‐lying minima, transition states connecting two local minima and corresponding intrinsic reaction coordinates on the potential energy surface are explored. We found that the Na Cl distances at the transitions states for the dissociation pathways were distributed in a relatively wide range of 2.7–3.7 Å and that the Na Cl distance at the transition state did not correlate with the commonly used solvation coordinates. This suggests that the definition of the transition states with specific structures as well as good reaction coordinate is very difficult for the ionic dissociation process even in a small water cluster. © 2018 Wiley Periodicals, Inc.     

A computational mechanistic study of the deamination reaction of melamine

A detailed computational study of the deamination reaction of melamine by OH^–, n H₂O/OH^–, n H₂O (where n = 1, 2, 3), and protonated melamine with H₂O, has been carried out using density functional theory and ab initio calculations. All structures were optimized at M06/6‐31G(d) level of theory, as well as with the B3LYP functional with each of the basis sets: 6‐31G(d), 6‐31 + G(d), 6‐31G(2df,p), and 6‐311++G(3df,3pd). B3LYP, M06, and ω B97XD calculations with 6‐31 + G(d,p) have also been performed. All structures were optimized at B3LYP/6‐31 + G(d,p) level of theory for deamination simulations in an aqueous medium, using both the polarizable continuum solvation model and the solvation model based on solute electron density. Composite method calculations have been conducted at G4MP2 and CBS‐QB3. Fifteen different mechanistic pathways were explored. Most pathways consisted of two key steps: formation of a tetrahedral intermediate and in the final step, an intermediate that dissociates to products via a 1,3‐proton shift. The lowest overall activation energy, 111 kJ mol^?1 at G4MP2, was obtained for the deamination of melamine with 3H₂O/OH^?.     

DFT 1H–1H coupling constants in the conformational analysis and stereoisomeric differentiation of 6‐heptenyl‐2H‐pyran‐2‐ones: configurational reassignment of synargentolide A

Density functional theory (DFT) ¹H–¹H NMR coupling constant calculations, including solvation parameters with the polarizable continuum model B3LYP/DGDZVP basis set together with the experimental values measured by spectral simulation, were used to predict the configuration of hydroxylated 6‐heptenyl‐5,6‐dihydro‐2H‐pyran‐2‐ones 1 , 2 , 4 , and 7 , allowing epimer differentiation. Modeling of these flexible compounds requires the inclusion of solvation models that account for stabilizing interactions derived from intramolecular and intermolecular hydrogen bonds, in contrast with peracetylated derivatives ( 3 , 5 , and 6 ) in which the solvation consideration can be omitted. Using this DFT NMR integrated approach as well as spectral simulation, the configurational reassignment of synargentolide A ( 8 ) was accomplished by calculations in the gas phase among four possible diastereoisomers ( 8–11 ). Calculated ³J_H,H values established its configuration as 6R‐[4′S,5′S,6′S‐(triacetyloxy)‐2E‐heptenyl]‐5,6‐dihydro‐2H‐pyran‐2‐one ( 8 ), in contrast with the incorrect 6R,4′R,5′R,6′R‐diastereoisomer previously proposed by synthesis ( 12 ). Application of this approach increases the probability for successful enantiospecific total syntheses of flexible compounds with multiple chiral centers. Copyright © 2014 John Wiley & Sons, Ltd.     

Insights into the dynamics of evaporation and proton migration in protonated water clusters from Large‐scale Born–Oppenheimer direct dynamics

Large‐scale on‐the‐fly Born–Oppenheimer molecular dynamics simulations using recent advances in linear scaling electronic structure theory and trajectory integration techniques have been performed for protonated water clusters around the magic number (H₂O)_nH⁺, for n = 20 and 21. Besides demonstrating the feasibility and efficiency of the computational approach, the calculations reveal interesting dynamical details. Elimination of water molecules is found to be fast for both cluster sizes but rather insensitive to the initial geometry. The water molecules released acquire velocities compatible with thermal energies. The proton solvation shell changes between the well‐known Eigen and Zundel motifs and is characterized by specific low‐frequency vibrational modes, which have been quantified. The proton transfer mechanism largely resembles that of bulk water but one interesting variation was observed. © 2012 Wiley Periodicals, Inc.     

Structural and Infrared Spectroscopic Study on Solvation of Acetylene by Protonated Water Molecules

The effect of solvation on the conformation of acetylene has been studied by adding one water molecule at a time. Quantum chemical calculations of the H⁺(C₂H₂)(H₂O)_n (n=1-5) clusters indicate that the H₂O molecules prefer to form the OH…π interaction rather than the CH…O interaction. This solvation motif is different from that of neutral (C₂H₂)(H₂O)_n (n=1-4) clusters, in which the H₂O molecules prefer to form the CH…O and OH…C H-bonds. For the H⁺(C₂H₂)(H₂O)_n cationic clusters, the first solvation shell consists of one ring structure with two OH…π H-bonds and three water molecules, which is completed at n=4. Simulated infrared spectra reveal that vibrational frequencies of OH…π H-bonded O-H stretching afford a sensitive probe for exploring the solvation of acetylene by protonated water molecules. Infrared spectra of the H⁺(C₂H₂)(H₂O)_n(n=1-5) clusters could be readily measured by the infrared photodissociation technique and thus provide useful information for the understanding of solvation processes.     

A DFT and TD‐DFT Approach to the Understanding of Statistical Kinetics in Substitution Reactions of M3Q4 (M=Mo,W; Q=S,Se) Cuboidal Clusters

For many years it has been known that the nine water molecules in [M₃Q₄(H₂O)₉]⁴⁺ cuboidal clusters (M=Mo, W; Q=S, Se) can be replaced by entering ligands, such as chloride or thiocyanate, and kinetic studies carried out mainly on the substitution of the first water molecule at each metal centre reveal that the reaction at the three metal centres occurs with statistical kinetics; that is, a single exponential with a rate constant corresponding to the reaction at the third centre is observed instead of the expected three‐exponential kinetic trace. Such simplification of the kinetic equations requires the simultaneous fulfilment of two conditions: first that the three consecutive rate constants are in statistical ratio, and second that the metal centres behave as independent chromophores. The validity of those simplifications has been checked for the case of the reaction of [Mo₃S₄(H₂O)₉]⁴⁺ with Cl^? by using DFT and TD‐DFT theoretical calculations. The results of those calculations are in agreement with the available experimental information, which indicates that the H₂O ligands trans to the μ‐S undergo substitution much faster than those trans to the μ₃‐S. Moreover, the energy barriers for the substitution of the first water molecule at the three metal centres are close to each other, the differences being compatible with the small changes in the numerical values of the rate constants required for observation of statistical kinetics. TD‐DFT calculations lead to calculated electronic spectra, which are in reasonable agreement with those experimentally measured, but the calculations do not indicate that the three metal centres behave as independent chromophores, although the mathematical conditions required for simplification of the kinetic traces to a single exponential are reasonably well fulfilled at certain wavelengths. A re‐examination of the kinetics of the reaction by using global fitting procedures yields results, which are compatible with statistical kinetics, although an alternative interpretation in which substitution only occurs at a single metal centre under reversible conditions is also possible.     

Experimentation with different thermodynamic cycles used for pKa calculations on carboxylic acids using complete basis set and Gaussian‐n models combined with CPCM continuum solvation methods

Complete basis set and Gaussian‐n methods were combined with Barone and Cossi's implementation of the polarizable conductor model (CPCM) continuum solvation methods to calculate pK_a values for six carboxylic acids. Four different thermodynamic cycles were considered in this work. An experimental value of ?264.61 kcal/mol for the free energy of solvation of H⁺, ΔG_s(H⁺), was combined with a value for G_gas(H⁺) of ?6.28 kcal/mol, to calculate pK_a values with cycle 1. The complete basis set gas‐phase methods used to calculate gas‐phase free energies are very accurate, with mean unsigned errors of 0.3 kcal/mol and standard deviations of 0.4 kcal/mol. The CPCM solvation calculations used to calculate condensed‐phase free energies are slightly less accurate than the gas‐phase models, and the best method has a mean unsigned error and standard deviation of 0.4 and 0.5 kcal/mol, respectively. Thermodynamic cycles that include an explicit water in the cycle are not accurate when the free energy of solvation of a water molecule is used, but appear to become accurate when the experimental free energy of vaporization of water is used. This apparent improvement is an artifact of the standard state used in the calculation. Geometry relaxation in solution does not improve the results when using these later cycles. The use of cycle 1 and the complete basis set models combined with the CPCM solvation methods yielded pK_a values accurate to less than half a pK_a unit. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Complexation of Cyclodextrins with Benzoic Acid in Water-Organic Solvents: A Solvation-Thermodynamic Approach

The aim of this research is to obtain new data about the complexation between β-cyclodextrin (β-CD) and benzoic acid (BA) as a model reaction of the complex formation of hydrophobic molecules with cyclodextrins (CDs) in various media. This research may help developing cyclodextrin-based pharmaceutical formulations through the choice of the appropriate solvent mixture that may be employed in the industrial application aiming to control the reactions/processes in liquid phase. In this paper, NMR results for the molecular complex formation between BA and β-CD ([BA⊂β-CD]) in D₂O-DMSO-d₆ and in D₂O-EtOH have shown that the stability of the complex in the H₂O-DMSO-d₆ varies within the experimental error, while decreases in H₂O-EtOH. Changes in the Gibbs energy of BA resolvation in water and water–dimethylsulfoxide mixtures have been obtained and have been used in the analysis of the reagent solvation contributions into the Gibbs energy changes of the [BA⊂β-CD] molecular complex formation. Quantum chemical calculations of the interaction energy between β-CD and BA as well as the structure of the [BA⊂β-CD] complex and the energy of β-CD and BA interaction in vacuum and in the medium of water, methanol and dimethylsulfoxide solvents are carried out. The stability of [BA⊂β-CD] complex in H₂O-EtOH and H₂O-DMSO solvents, obtained by different methods, are compared. The thermodynamic parameters of the [BA⊂β-CD] molecular complexation as well as the reagent solvation contributions in H₂O-EtOH and H₂O-DMSO mixtures were analyzed by the solvation-thermodynamic approach.     

Two pseudopolymorphic hydrates of brucine: brucine–water (1/4) and brucine–water (1/5.25) at 130 K

The structures of two pseudopolymorphic hydrates of brucine, C₂₃H₂₆N₂O₄·4H₂O, (I), and C₂₃H₂₆N₂O₄·5.25H₂O, (II), have been determined at 130 K. In both (I) and (II) (which has two independent brucine mol­ecules together with 10.5 water mol­ecules of solvation in the asymmetric unit), the brucine mol­ecules form head‐to‐tail sheet substructures, which associate with the water mol­ecules in the inter­stitial cavities through hydrogen‐bonding associations and, together with water–water associations, give three‐dimensional framework structures.     

Ligand Exchange Processes on Solvated Beryllium Cations. IV [Be(H2O)2(imidazole‐based Chelate)]1)

The water exchange reaction of [Be(H₂O)₂(1H‐imidazole‐4,5‐dicarboxylate)] and [Be(H₂O)₂(1H‐imidazol‐3‐ium‐4,5‐dicarboxylate)]⁺ in water was studied by DFT calculations (RB3LYP/6‐311+G**) and identified as an associative interchange mechanism. The activation barriers for [Be(H₂O)₂(1H‐imidazole‐4,5‐dicarboxylate)] (16.6 kcal/mol) and [Be(H₂O)₂(1H‐imidazol‐3‐ium‐4,5‐dicarboxylate)]⁺ (13.8 kcal/mol) are similar to the barrier for [Be(H₂O)₄)]²⁺ and independent of the overall charge. NICS calculations show no indication that the aromaticity of the imidazole ring is affected during the water exchange process.     

Alaninyl­tryptophan hydrate,glycyl­tryptophan dihydrate and tryptophyl­glycine hydrate

The crystal structures of the title tryptophan‐containing dipeptides, C₁₄H₁₇N₃O₃·H₂O, (I), C₁₃H₁₅N₃O₃·2H₂O, (II), and C₁₃H₁₅N₃O₃·H₂O, (III), respectively, contain at least one water mol­ecule of solvation. As a result, the crystal packing of these compounds is composed of regions of water‐mediated hydrogen bonding and tryptophan ring‐to‐ring stacking separated by the length of the mol­ecule. The tryptophan rings stack in a continuous layer that, when viewed edge‐on from the outermost part of the tryptophan ring, exhibits a herring‐bone motif. However, owing to the lack of direct overlap of adjacent rings, no degree of π contact or long‐range delocalization of ring systems is possible here. The overall molecular conformations of (I) and (III) contain a folding of one peptide over the other, such that a minimum in molecular volume occurs without any intramolecular hydrogen bonding. In these two dipeptides, extensive hydrogen bonding is observed to and from the single water mol­ecule of solvation. In the crystal structure of (II), however, an extended mol­ecule conformation complements a more extensive hydrogen‐bonding scheme involving two water mol­ecules of solvation per dipeptide.     

Competing Insertion and External Binding Motifs in Hydrated Neurotransmitters: Infrared Spectra of Protonated Phenylethylamine Monohydrate

Hydration has a drastic impact on the structure and function of flexible biomolecules, such as aromatic ethylamino neurotransmitters. The structure of monohydrated protonated phenylethylamine (H⁺PEA?H₂O) is investigated by infrared photodissociation (IRPD) spectroscopy of cold cluster ions by using rare‐gas (Rg=Ne and Ar) tagging and dispersion‐corrected density functional theory calculations at the B3LYP‐D3/aug‐cc‐pVTZ level. Monohydration of this prototypical neurotransmitter gives an insight into the first step of the formation of its solvation shell, especially regarding the competition between intra‐ and intermolecular interactions. The spectra of Rg‐tagged H⁺PEA?H₂O reveal the presence of a stable insertion structure in which the water molecule is located between the positively charged ammonium group and the phenyl ring of H⁺PEA, acting both as a hydrogen bond acceptor (NH⁺???O) and donor (OH???π). Two other nearly equivalent isomers, in which water is externally H bonded to one of the free NH groups, are also identified. The balance between insertion and external hydration strongly depends on temperature.     

Water oxidation on N‐Doped TiO2 nanotube arrays

Photocatalytic splitting water into hydrogen and oxygen by utilizing solar energy is regarded as an effective strategy to solve oil crisis. By utilizing density functional calculations, we herein present the systemic studies with respect to water splitting mechanism on N‐doped TiO₂ nanotube arrays (NTAs), and focus on activation energy, thermodynamic properties, and effects of N‐doping on reaction process. Our results reveal that the impurity 2p states of doped nitrogen effectively change electronic structure of TiO₂ NTAs, which act as an electron acceptor and facilitate weakly bound electrons of valence band to be easily excited to acceptor level, as well as enhance the first H₂O adsorption and dissociation on the inside wall of N‐doped TiO₂ NTAs. Therefore, it is found that the rate‐determining step of water splitting is the formation reaction of HOO* on N‐doped TiO₂ NTAs rather than the formation of HO* from the first H₂O. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Potential energy surface of the reaction of imidazole with peroxynitrite: Density functional theory study

This article presents a theoretical investigation of the reaction mechanism of imidazole nitration by peroxynitrite using density functional theory calculations. Understanding this reaction mechanism will help in elucidating the mechanism of guanine nitration by peroxynitrite, which is one of the assumed chemical pathways for damaging DNA in cells. This work focuses on the analysis of the potential energy surface (PES) for this reaction in the gas phase. Calculations were carried out using Hartree–Fock (HF) and density functional theory (DFT) Hamiltonians with double‐zeta basis sets ranging from 6‐31G(d) to 6‐31++G(d,p), and the triple‐zeta basis set 6‐311G(d). The computational results reveal that the reaction of imidazole with peroxynitrite in gas phase produces the following species: (i) hydroxide ion and 2‐nitroimidazole, (ii) hydrogen superoxide ion and 2‐nitrosoimidazole, and (iii) water and 2‐nitroimidazolide. The rate‐determining step is the formation of a short‐lived intermediate in which the imidazole C₂ carbon is covalently bonded to peroxynitrite nitrogen. Three short‐lived intermediates were found in the reaction path. These intermediates are involved in a proton‐hopping transport from C₂ carbon to the terminal oxygen of the ? O? O moiety of peroxynitrite via the nitroso (ON? ) oxygen. Both HF and DFT calculations (using the Becke3–Lee–Yang–Parr functional) lead to similar reaction paths for proton transport, but the landscape details of the PES for HF and DFT calculations differ. This investigation shows that the reaction of imidazole with peroxynitrite produces essentially the same types of products (nitro‐ and nitroso‐) as observed experimentally in the reaction of guanine with peroxynitrite, which makes the former reaction a good model to study by computation the essential characteristics of the latter reaction. Nevertheless, the computationally determined activation energy for imidazole nitration by peroxynitrite in the gas phase is 84.1 kcal/mol (calculated at the B3LYP/6‐31++G(d,p) level), too large for an enzymatic reaction. Exploratory calculations on imidazole nitration in solution, and on the reaction of 9‐methylguanine with peroxynitrite in the gas phase and solution, show that solvation increases the activation energy for both imidazole and guanine, and that the modest decrease (15 kcal mol^?1) in the activation energy, due to the adjacent six member ring of guanine, is counterbalanced by solvation. These results lead to the speculation that proton tunneling may be at the origin of experimentally observed high reaction rate of guanine nitration by peroxynitrite in solution. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Gas‐Phase Kinetics of Chlorosilylene Reactions II. ClSiH + C2H4: Absolute Rate Measurements and Quantum Chemical and RRKM Calculations for the Prototype π Addition Reaction

Time‐resolved studies of chlorosilylene, ClSiH, generated by the 193 nm laser flash photolysis of 1‐chloro‐1‐silacyclopent‐3‐ene, are carried out to obtain rate constants for its bimolecular reaction with ethene, C₂H₄, in the gas‐phase. The reaction is studied over the pressure range 0.13–13.3 kPa (with added SF₆) at five temperatures in the range 296–562 K. The second order rate constants, obtained by extrapolation to the high pressure limits at each temperature, fitted the Arrhenius equation: log(k^∞/cm³ molecule^?1 s^?1)=(?10.55±0.10) + (3.86±0.70) kJ mol^?1/RT ln10. The Arrhenius parameters correspond to a loose transition state and the rate constant at room temperature is 43 % of that for SiH₂ + C₂H₄, showing that the deactivating effect of Cl‐for‐H substitution in the silylene is not large. Quantum chemical calculations of the potential energy surface for this reaction at the G3MP2//B3LYP level show that, as well as 1‐chlorosilirane, ethylchlorosilylene is a viable product. The calculations reveal how the added effect of the Cl atom on the divalent state stabilisation of ClSiH influences the course of this reaction. RRKM calculations of the reaction pressure dependence suggest that ethylchlorosilylene should be the main product. The results are compared and contrasted with those of SiH₂ and SiCl₂ with C₂H₄.     

Ligand Exchange Processes on Solvated Beryllium Cations. II [Be(solvent)(12‐Crown‐4)]2+

The solvation and solvent exchange mechanism of [Be(12‐crown‐4)]²⁺ in water and ammonia was studied by DFT calculations (RB3LYP/6‐311+G**). In solution, five‐fold coordinated Be²⁺ species of quadratic pyramidal [Be(H₂O)(12‐crown‐4)]²⁺ and [Be(NH₃)(12‐crown‐4)]²⁺ exist. The water and ammonia exchange reactions follow an associative interchange mechanism, similar to that found for the pure solvent complexes [Be(H₂O)₄]²⁺ and [Be(NH₃)₄]²⁺. The activation barriers are clearly smaller than for the pure solvent complexes, viz. [Be(H₂O)(12‐crown‐4)]²⁺: 6.0 kcal/mol and [Be(NH₃)(12‐crown‐4)]²⁺: 15.3 kcal/mol.     

Hydrogen bonding in brucinium dihydrogen citrate trihydrate at 130 K

The structure of brucinium dihydrogen citrate trihydrate (systematic name: 2,3‐dimeth­oxy‐10‐oxostrychnidinium dihydrogen citrate trihydrate), C₂₃H₂₇N₂O₄⁺·C₆H₇O₇⁻·3H₂O, has been determined at 130 K. The crystallographic asymmetric unit comprises two brucinium cations, two dihydrogen citrate anions and six water mol­ecules of solvation. The two citrate anions, which are conformationally dissimilar, associate through extensive hydrogen‐bonding inter­actions with the common undulating brucinium cation layer substructures and the water mol­ecules, forming a three‐dimensional framework polymer.     

A Computational Understanding of Solvent Effect on the Structure,Electronic, Thermochemical,and Spectroscopic Properties of Ni(η2‐C6H4)(H2PCH2CH2PH2) Complex

Here we report the density functional calculations of the molecular parameters including the energy, geometries, electric dipole moments, vibrational IR frequencies, and ¹H and ¹³C NMR chemical shifts of Ni(η²‐C₆H₄ )(H₂PCH₂CH₂PH₂ ) (a benzyne complex). Based on the polarizable continuum model (PCM ), the effect of polarity of the solvent on these parameters was explored. The wavenumbers of υ(C1–C2 ) as well as the ¹H and ¹³C NMR chemical shift values of complex in various solvents were calculated and correlated with the Kirkwood–Bauer–Magat equation (KBM ), the solvent acceptor numbers (ANs ), and the linear solvation energy relationship (LSER ). The bonding interaction between the benzyne and Ni(H₂PCH₂CH₂PH₂ ) fragment was analyzed by means of the energy decomposition analysis (EDA ). The character of the Ni–C bonds of the molecules was analyzed by natural bond orbital (NBO ) analysis. Also, Monte Carlo simulations were used for the calculation of the total energy and solvation free energy of the complex in water.