Thermodynamics and kinetics of imidazole formation from glyoxal, methylamine, and formaldehyde: a computational study

Density functional theory calculations, including Poisson-Boltzmann implicit solvent and free energy corrections, are applied to study the mechanism of experimentally observed imidazole formation from the reaction of glyoxal and methylamine in solution. Our calculations suggest that a diimine species is an important intermediate in the reaction. Under acidic conditions, we find that the diimine acts as a nucleophile in attacking the carbonyl group of either formaldehyde or glyoxal to first generate an acyclic enol intermediate, which then goes on to close the ring and form imidazoles. Our results confirm that formaldehyde and, by extension, other small aldehydes are likely to be incorporated into imidazole ions in the presence of glyoxal and primary amines in clouds and aqueous aerosol. This is a new mechanism of aerosol formation by formaldehyde, the most abundant aldehyde in the atmosphere. The amount of aerosol formed will depend on the amounts of glyoxal and amines present.     

Thermodynamics and kinetics of methylboroxine.amine adduct formation: a computational study

Density functional theory (B3LYP//6-311+G*) calculations including Poisson-Boltzmann implicit solvent were applied to study the formation of the trimethylboroxine.amine adduct with respect to methylboronic acid monomers and free amine in solution. Potential intermediates and transition states between intermediates were calculated to assess the thermodynamic and kinetic factors controlling this transformation. Our calculations suggest that the rate-determining steps are condensation reactions to form dimers and trimers, and closure of the boroxine ring. Fast amine exchange is expected throughout the transformation, and the most-stable intermediate is a dimer.amine adduct. Using our calculated barriers for the methyl system as a template, we assess the conversion of phenylboronic acid to the triphenylboroxine.amine adduct and find that the pathway is most likely similar, except that the transformation is thermodynamically and kinetically more favored for the phenyl system in the presence of pyridine.     

Thermodynamics of peptide dimer formation

The Replica Exchange Statistical Temperature Molecular Dynamics algorithm is used to study the equilibrium properties of a peptide monomer and dimer and the thermodynamics of peptide dimer formation. The simulation data are analyzed by the Statistical Temperature Weighted Histogram Analysis Method. Each 10-residue peptide is represented by a coarse-grained model with hydrophobic side chains and has an α-helix as its minimum energy configuration. It is shown that the configurational behavior of the dimer can be divided into four regions as the temperature increases: two folded peptides; one folded and one unfolded peptide; two unfolded peptides; and two spatially separated peptides. Two important phenomena are discussed: in the dimer, one peptide unfolds at a lower temperature than the isolated monomer and the other peptide unfolds at a higher temperature than the isolated monomer. In addition, in the temperature region where one peptide is folded and the other unfolded, the unfolded peptide adopts an extended structure that minimizes the overall surface area of the aggregate. It is suggested that combination of destabilization due to aggregation and the resulting extended configuration of the destabilized peptide could have implications for nucleating β-sheet structures and the ultimate formation of fibrils.     

A computational study of the LiH dimer

A theoretical study of the properties of the linear LiH dimer was undertaken. In this dimer, an unusual type of hydrogen bonding (termed "inverse" hydrogen bonding by some authors), which involves the hydrogen bonded molecule acting as an electron donor (rather than as a proton donor), is exhibited. The optimized geometry, dipole moment, interaction energy, atomic charges, harmonic vibrational frequencies, and frequency shifts for the dimer are computed at the SCF, MP2, and QCISD levels of theory using mainly a 6-31++G(d,p) basis set. We also examined the relative stability of the mono-deuterated isotopomers of linear (LiH)(2), i.e., Li-H...Li-D and Li-D...Li-H. Analysis of the normal vibrational modes, changes in the partial atomic charges, and changes in the vibrational frequencies of LiH on complexation were used to gain insight into the bonding and properties of the linear LiH dimer and its isotopomers.     

Thermodynamics and kinetics of atmospheric aerosol particle formation and growth

In this tutorial review we summarize the standard approaches to describe aerosol formation from atmospheric vapours and subsequent growth - with a particular emphasis on the interplay between equilibrium thermodynamics and non-equilibrium transport. We review the use of thermodynamics in describing phase equilibria and formation of aerosol particles from supersaturated vapour via nucleation. We also discuss the kinetics of cluster formation and transport phenomena, which are used to describe dynamic mass transport between the gaseous and condensed phases in a non-equilibrium system. Finally, we put these theories into the context of atmospheric observations of aerosol formation and growth.     

Time-resolved study of thymine dimer formation

The formation of thymine dimers in the single-stranded oligonucleotide, (dT)20, is studied at room temperature by laser flash photolysis using 266 nm excitation. It is shown that the (6-4) adduct is formed within 4 ms via a reactive intermediate. The formation of cyclobutane dimers is faster than 200 ns. The overall quantum yield for the (6-4) formation is (3.7 +/- 0.3) x 10-3, and that of the cyclobutane dimers is (2.8 +/- 0.2) x 10-2. No triplet absorption is detected, showing that either the intersystem crossing yield decreases by 1 order of magnitude upon oligomerization (<1.4 x 10-3) or the triplet state reacts with unit efficiency in less than 200 ns to yield cyclobutane dimers.     

Excited state complex formation between methyl glyoxal and some aromatic bio-molecules: a fluorescence quenching study

Fluorescence quenching of some important aromatic bio-molecules (ABM) such as 3-aminophthalhydrazide (luminol), tryptophan (Try), phenylalanine and tyrosine (Tyr) by methyl glyoxal (MG) has been studied employing different spectroscopic techniques. The interaction of MG with ABM in the excited state has been analysed using Stern-Volmer (S-V) mechanism. In the case of MG-luminol system time correlated single photon counting (TCSPC) technique has also been applied to explain the S-V mechanism. The bimolecular rate constants obtained are found to be higher than the rate constant for diffusion controlled process. A plausible explanation of the quenching mechanism has been discussed on the basis of hydrogen bonding, charge transfer and energy transfer interaction between the colliding species.     

Hydrogen-bonded dimer can mediate supramolecular β-sheet formation and subsequent amyloid-like fibril formation: a model study

FT-IR data of six terminally blocked tripeptides containing Acp (ε-aminocaproic acid) reveals that all of them form supramolecular β-sheets in the solid state. Single crystal X-ray diffraction studies of two peptides not only support this data but also disclose the fact that the supramolecular β-sheet formation is initiated via dimer formation. The Scanning Electron Microscopic images of all peptides exhibit amyloid-like fibrils that show green birefringence after binding with Congo red, which is a characteristic feature of many neurodegenerative disease causing amyloid fibrils.     

Free energy perturbation study of water dimer dissociation kinetics

An efficient approach is described for using accurate ab initio calculations to determine the rates of elementary condensation and evaporation processes that lead to nucleation of aqueous aerosols. The feasibility of the method is demonstrated in an application to evaporation rates of water dimer at 230 K. The method, known as ABC-FEP (ab initio/classical free energy perturbation), begins with a calculation of the potential of mean force for the dissociation (evaporation) of small water clusters using a molecular dynamics (MD) simulation with a model potential. The free energy perturbation is used to calculate how changing from the model potential to a potential calculated from ab initio methods would alter the potential of mean force. The difference in free energy is the Boltzmann-weighted average of the difference between the ab initio and classical potential energies, with the average taken over a sample of configurations from the MD simulation. In principle, the method does not require a highly accurate model potential, though more accurate potentials require fewer configurations to achieve a small sampling error in the free energy perturbation step. To test the feasibility of obtaining accurate potentials of mean force from ab initio calculations at a modest number of configurations, the free energy perturbation method has been used to correct the errors when some standard models for bulk water (SPC, TIP4P, and TIP4PFQ) are applied to water dimer. To allow a thorough exploration of sampling issues, a highly accurate fit to results of accurate ab initio calculations, known as SAPT-5s, as been used a proxy for the ab initio calculations. It is shown that accurate values for a point on the potential of mean force can be obtained from any of the water models using ab initio calculations at only 50 configurations. Thus, this method allows accurate simulations of small clusters without the need to develop water models specifically for clusters.     

Mechanism and diastereoselectivity of aziridine formation from sulfur ylides and imines: a computational study

A computational investigation of the title reaction involving semistabilized (R = Ph) and stabilized (R = CO2Me) sulfur ylides has been performed using DFT methods including a continuum model of solvent. Our results provide support for the generally accepted mechanism and are in very good agreement with observed cis/trans selectivities. This study shows that betaine formation is nonreversible, and that selectivity is thereby determined at the initial addition step, in the case of semistabilized ylides. Our analysis indicates moreover that addition TS structures are governed by the steric strain induced by the N-sulfonyl group, which favors the transoid approach in the case of syn betaine formation and the cisoid mode of addition in anti TSs. The observed low trans selectivity is accounted for by the favorable Coulombic interactions and stabilization by C-H...O hydrogen bonding allowed in the cisoid anti addition TS. In the case of stabilized ylides, the endothermicity of betaine formation combined with the high barrier to ring closure render the elimination step rate- and selectivity-determining. Accordingly, the low cis selectivity observed in stabilized ylide reactions is explained by the lower steric strain in the elimination step generated by the formation of the cis aziridine (as compared to the trans case).     

Antioxidant activity of trans-resveratrol toward hydroxyl and hydroperoxyl radicals: a quantum chemical and computational kinetics study

In this work, we have carried out a systematic study of the antioxidant activity of trans-resveratrol toward hydroxyl ((?)OH) and hydroperoxyl ((?)OOH) radicals in aqueous simulated media using density functional quantum chemistry and computational kinetics methods. All possible mechanisms have been considered: hydrogen atom transfer (HAT), proton-coupled electron transfer (PCET), sequential electron proton transfer (SEPT), and radical adduct formation (RAF). Rate constants have been calculated using conventional transition state theory in conjunction with the Collins-Kimball theory. Branching ratios for the different paths contributing to the overall reaction, at 298 K, are reported. For the global reactivity of trans-resveratrol toward (?)OH radicals, in water at physiological pH, the main mechanism of reaction is proposed to be the sequential electron proton transfer (SEPT). However, we show that trans-resveratrol always reacts with (?)OH radicals at a rate that is diffusion-controlled, independent of the reaction pathway. This explains why trans-resveratrol is an excellent but very unselective (?)OH radical scavenger that provides antioxidant protection to the cell. Reaction between trans-resveratrol and the hydroperoxyl radical occurs only by phenolic hydrogen abstraction. The total rate coefficient is predicted to be 1.42 × 10(5) M(-1) s(-1), which is much smaller than the ones for reactions of trans-resveratrol with (?)OH radicals, but still important. Since the (?)OOH half-life time is several orders larger than the one of the (?)OH radical, it should contribute significantly to trans-resveratrol oxidation in aqueous biological media. Thus, trans-resveratrol may act as an efficient (?)OOH, and also presumably (?)OOR, radical scavenger.     

The association reaction between C2H and 1-butyne: a computational chemical kinetics study

The potential energy surfaces (PES) for the reaction of the C(2)H radical with 1-butyne (C(4)H(6)) have been studied using the CBS-QB3 method. Density functional B3LYP/cc-pVTZ and M06-2X/6-311++G(d,p) calculations have also been performed to analyze the reaction energetics. For detailed theoretical calculation on the total reaction mechanism, the initial association reactions on more and less substituted C atoms of 1-butyne are treated separately followed by a variational transition state theory (VTST) calculation to obtain reaction rates. The successive unimolecular reactions from the association reaction complexes are subjected to Rice-Ramsperger-Kassel-Marcus (RRKM) calculations for reaction rate constants and product branching ratios. The calculated rate constants in the temperature range 70-295 K for both the association reactions are found to be highly temperature dependent at low temperatures, which is contrary to the experimental findings of temperature independent association rates. We have explained this observation with the help of variational nature of the transition states, and we found a "loose" transition state at low temperatures. The calculated product branching ratios for the unimolecular reactions generally agree with the available experimental data, although some channels show a significant method dependency and therefore the correlation with experiment is lost to some extent. Our detailed reaction energetics calculations confirm that the C(2)H + C(4)H(6) reaction proceeds without an entrance barrier and leads to the important products ethynylallene + CH(3), 1,3-hexadiyne + H, 3,4-hexadiene-1-yne + H, 2-ethynyl-1,3-butadiene + H, 3,4-dimethylenecyclobut-1-ene + H and fulvene + H exothermic by 25-75 kcal mol(-1), with strong dependence of the product distribution on the association mode of C(2)H with C(4)H(6), making these reactions fast under low temperature conditions of Titan's atmosphere. Therefore this study can provide a detailed picture of the complex hydrocarbon formation mechanism in the upper atmosphere.     

Favoring heterotrimeric boroxine formation using an internal Lewis base: a computational study

Heterotrimeric arylboroxines can be favorably formed by designing one of the arylboronic acid monomers to contain a pendant Lewis base. Using density functional theory (B3LYP//6-311+G*) calculations including Poisson-Boltzmann implicit solvent, we found that AB2 trimeric arylboroxines were thermodynamically favored over A2B, A3, or B3, where A and B are monomeric arylboronic acids with and without a pendant Lewis base, respectively. The most stable AB2 trimers were formed when the B monomer contained electron-withdrawing substituents, particularly halogens in the para-position or pi-acceptors in the meta-position. On the other hand, adding different para-substituents to the A monomer did not significantly change the energetics. Our calculations also suggest that ABC trimers with three different monomers will not be significantly favored over AB2 trimers when making small electronic perturbations, by changing the substituents on each monomer.     

Thermodynamics and kinetics of bubble nucleation: Simulation methodology

The simulation of homogeneous liquid to vapor nucleation is investigated using three rare-event algorithms, boxed molecular dynamics, hybrid umbrella sampling Monte Carlo, and forward flux sampling. Using novel implementations of these methods for efficient use in the isothermal-isobaric ensemble, the free energy barrier to nucleation and the kinetic rate are obtained for a Lennard-Jones fluid at stretched and at superheated conditions. From the free energy surface mapped as a function of two order parameters, the global density and largest bubble volume, we find that the free energy barrier height is larger when projected over bubble volume. Using a regression analysis of forward flux sampling results, we show that bubble volume is a more ideal reaction coordinate than global density to quantify the progression of the metastable liquid toward the stable vapor phase and the intervening free energy barrier. Contrary to the assumptions of theoretical approaches, we find that the bubble takes on cohesive non-spherical shapes with irregular and (sometimes highly) undulating surfaces. Overall, the resulting free energy barriers and rates agree well between the methods, providing a set of complementary algorithms useful for studies of different types of nucleation events.     

Kinetic study of proton-bound dimer formation using ion mobility spectrometry

A method to measure the rate constant for the formation of symmetrical proton-bound dimers at ambient pressure was proposed. The sample is continuously delivered to the drift region of an ion mobility spectrometer where it reacts with a swarm of monomer ions injected by the shutter grid. Dimer ions are formed in the drift tube and a tail appears in the ion mobility spectrum. The rate constant is derived from the mobility spectra. The proposed approach was typically examined for methyl isobutyl ketone (MIBK), 2,4-dimethyl pyridine (DMP), and dimethyl methyl phosphonate (DMMP). The rate constants measured in this study were: 0.25 × 10⁻⁹, 0.86 × 10⁻¹⁰, and 0.47 × 10⁻¹⁰ cm³ s⁻¹ for MIBK, DMP and DMMP, respectively. The logarithm of the measured rate constants were found to be almost independent of reciprocal temperature within 303 to 343 K, indicating that no activation energy is involved in the formation of proton-bound dimers.     

Monosilicon-substituted cyanoacetylene: a computational study

A detailed theoretical investigation of the [H,Si,C(2),N] potential energy surfaces including 28 minimum isomers and 65 interconversion transition states is reported at the Gaussian-3//B3LYP/6-31G(d) level. Generally, the triplet species lie energetically higher than the singlet ones. The former three low-lying isomers are linear HCCNSi 1 (0.00 kcal/mol), branched SiC(H)CN 12 (7.09 kcal/mol), and bent HNCCSi 7 (14.22 kcal/mol), which are separated by rather high barriers from each other and are kinetically very stable with the least conversion barriers of 32.6-70.5 kcal/mol. Two energetically high-lying isomers HCNCSi 3 (42.99 kcal/mol) and SiC(H)NC 13 (36.05 kcal/mol) are also kinetically stable with a barrier of 49.19 and 21.42 kcal/mol, respectively. Additionally, five high-lying isomers, that is, three chainlike isomers, HCCSiN 2 (55.17), HCSiNC 6 (47.80), HSiNCC 11 (78.83), and one three-membered ring isomer HN-cSiCC 19 (51.21), and one four-membered ring isomer cSiCN(H)C 27 (50.6 kcal/mol), are predicted to each have lower conversion barriers of 12-18 kcal/mol and can be considered as meta-stable species. All of the predicted 10 isomers could exist as stable or meta-stable intermediates under suitable conditions. Finally, the structural and bonding analysis indicate that the [H,Si,C(2),N] molecule contains various properties that are of chemical interest (e.g., silylene, SiC triple bonding, and conjugate SiN triple bonding and CC triple bonding, charge-transfer specie, planar aromatic specie, cumulate double bonding). This is the first detailed theoretical study on the potential energy surfaces of the series of hydrogenated Si,C,C,N-containing molecules. The knowledge of the present monohydrogenated SiC(2)N isomerism could provide useful information for more highly hydrogenated or larger Si,C(2),N-containing species.     

Thermodynamics and kinetics of PNA-DNA quadruplex-forming chimeras

PNA-DNA chimeras present the interesting properties of PNA, such as the high binding affinity to complementary single-strand (DNA or RNA), and the resistance to nuclease and protease degradation. At the same time, the limitations of an oligomer containing all PNA residues, such as low water solubility, self-aggregation, and low cellular uptake, are effectively overcome. Further, PNA-DNA chimeras possess interesting biological properties as antisense agents. We have explored the ability of PNA-DNA chimeric strands to assemble in quadruplex structures. The rate constant for association of the quadruplexes and their thermodynamic properties have been determined by CD spectroscopy and differential scanning calorimetry (DSC). Thermal denaturation experiments indicated higher thermal and thermodynamic stabilities for chimeric quadruplexes in comparison with the corresponding unmodified DNA quadruplex. Singular value decomposition analysis (SVD) suggests the presence of kinetically stable intermediate species in the quadruplex formation process. The experimental results have been discussed on the basis of molecular dynamic simulations. The ability of PNA-DNA chimeras to form stable quadruplex structures expands their potential utility as therapeutic agents.     

Thermodynamics of patina formation

Changes in the standard Gibbs energies in reactions that occur in the interaction of copper and copper oxides with oxygen, water, and impurities contained in atmospheric precipitations were calculated.     

Unexpected formation of benziphthalocyanine dimer: An easily synthesizable dimer of phthalocyanine analogue

Methylene-bridged benziphthalocyanine dimer 2 was unexpectedly generated by the reaction of dihydroxybenziphthalocyanine 1 and formaldehyde in the presence of a catalytic amount of a base at room temperature. Single-crystal X-ray diffraction analysis of 2 revealed a V-shaped structure. Dimer 2 exhibited longer-wavelength absorption and fluorescence bands than monomer 1 in the near-IR region.