The influence of the quencher concentration on the rate of simple bimolecular reaction: molecular dynamics study

The paper presents the results of large-scale molecular dynamics simulations of the irreversible bimolecular reaction A+B --> C+B for the simple liquid composed of mechanically identical soft spheres. The systems with the total number of molecules corresponding to 10(7)-10(9) are considered. The influence of the concentration of a quencher (B) on the surviving probability of A and the reaction rate is analyzed for a wide range of the concentrations and for two significantly different reduced densities. It is shown that the quencher concentration dependence effect (QCDE) is, in fact, a composition of two QCDE effects: the short-time QCDE that increases the reaction rate and the long-time QCDE that decreases it. The paper also analyzes the influence of the concentration on the steady-state rate constant, k(ss), obtained by integrating the surviving probability. The excess in k(ss) due to finite quencher concentration changes the sign from negative to positive while going from low to high concentrations. Generally, the excess is extremely weak. It attains a 1% level only if the concentration is very high.     

The influence of the quencher concentration on the rate of simple bimolecular reaction: molecular dynamics study. II

In this paper new results of the simulations [M. Litniewski, J. Chem. Phys. 123, 124506 (2005)] on the influence of the quencher concentration on the reaction A+B-->C+B for the identical soft sphere system are presented. The problem is generalized by considering also the case when the spheres are immersed in the Brownian medium. A significant difference between simple deterministic systems and the Brownian ones is found: the excess in the rate coefficient for the Brownian system is constant and positive, except for very short times. The reaction has been simulated for a very long time, but any tendency to decrease the excess has not been noted. It is also shown that the relative excess in the surviving probability is a universal quadratic function of the quencher concentration for the range of time much longer than the result from the previous simulations. A very strong correlation between the excess in the relative value of spatial correlations between the reagents and the excess in the rate coefficient is shown. It is also shown that the A-A and A-C interactions have some influence on the excess values. A simple model for this effect is presented.     

Stability of nucleic acid base pairs in organic solvents: molecular dynamics, molecular dynamics/quenching, and correlated ab initio study

The dynamic structure and potential energy surface of adenine...thymine and guanine...cytosine base pairs and their methylated analogues interacting with a small number (from 1 to 16 molecules) of organic solvents (methanol, dimethylsulfoxide, and chloroform) were investigated by various theoretical approaches starting from simple empirical methods employing the Cornell et al. force field to highly accurate ab initio quantum chemical calculations (MP2 and particularly CCSD(T) methods). After the simple molecular dynamics simulation, the molecular dynamics in combination with quenching technique was also used. The molecular dynamics simulations presented here have confirmed previous experimental and theoretical results from the bulk solvents showing that, whereas in chloroform the base pairs create hydrogen-bonded structures, in methanol, stacked structures are preferred. While methanol (like water) can stabilize the stacked structures of the base pairs by a higher number of hydrogen bonds than is possible in hydrogen-bonded pairs, the chloroform molecule lacks such a property, and the hydrogen-bonded structures are preferred in this solvent. The large volume of the dimethylsulfoxide molecule is an obstacle for the creation of very stable hydrogen-bonded and stacked systems, and a preference for T-shaped structures, especially for complexes of methylated adenine...thymine base pairs, was observed. These results provide clear evidence that the preference of either the stacked or the hydrogen-bonded structures of the base pairs in the solvent is not determined only by bulk properties or the solvent polarity but rather by specific interactions of the base pair with a small number of the solvent molecules. These conclusions obtained at the empirical level were verified also by high-level ab initio correlated calculations.     

Ab initio molecular dynamics study of the hydrolysis reaction of diborane

The hydrolysis reaction of the diborane molecule in aqueous solution has been studied by a series of Car-Parrinello Molecular Dynamics simulations in the Blue Moon Ensemble. The total reaction has been divided into two parts: one dealing with the breaking of B(2)H(6) molecule and the formation of a BH(4)(-) ion, a H(2)BOH molecule and a H(+) ion; the second leads to the formation of two hydrogen molecules and another H(2)BOH molecule, starting from BH(4)(-), two water molecules and a H(+) ion. The total reaction studied in this work has been B(2)H(6) + 2H(2)O --> 2H(2)BOH + 2H(2). We have described both structurally and electronically the reagents and the products through the radial distribution functions and the Wannier Function Center positions calculations, with attention to the solvent effects on the compounds. The free energy barrier value for the first part of the reaction and a detailed mechanisms for both parts have been reported. An interesting behavior of BH(3) and H(2) molecules in solution has been observed. They form a quite stable three center bond between the electron pair of the hydrogen molecule and the empty orbital of the boron atom in BH(3), which has been described from both a structural and electronic point of view.     

Effect of temperature on the interactions between cellulose and lignin via molecular dynamics simulations

Cellulose - Heating is essential in various biomass pre-treatments and thermal conversion processes. It is of practical significance to study the characteristics of cellulose-lignin and...     

The influence of changes in the dipole moment of reagents on the rate of photoinduced electron transfer

The influence of spatial charge redistribution modeled by a change in the dipole moment of the reagent that experiences excitation on the dynamics of ultrafast photoinduced electron transfer was studied. A two-center model based on the geometry of real molecules was suggested. The model described photoexcitation and subsequent electron transfer in a donor-acceptor pair. The rate of electron transfer was shown to depend substantially on the dipole moment of the donor at the photoexcitation stage and the direction of subsequent electron transfer. These parameters also determined the most important characteristic of ultrafast photoinduced electron transfer, the angle ? between the reaction coordinates corresponding to these reaction stages. The regions of model parameters corresponding to the strongest influence of the carrier frequency of the exciting pulse on the rate of electron transfer were established.     

Theory of solvent influence on reaction dynamics

A generalization of the recently published quantum-classical approximation [A. A. Neufeld, J. Chem. Phys., 119, 2488 (2003)] for the purposes of reaction dynamics in condensed phase is presented. The obtained kinetic equations treat a solvent influence in a nonphenomenological way, account for the change of the free energy of the surrounding media, allow for different solvent dynamics in each reaction channel, and constitute a powerful framework for an accurate modeling of solvent effects, including ultrafast processes. The key features of the approach are its differential form, which considerably facilitates practical applications, and well defined wide applicability limits. The developed methodology fully accounts for an arbitrary long memory of the canonical bath and covers solvent-induced processes from a subpicosecond time scale.     

Understanding the Hofmeister effect in interactions between chaotropic anions and lipid bilayers: molecular dynamics simulations

A set of all-atom molecular dynamics simulations have been performed to better understand critical phenomena regarding a Hofmeister series of anions and lipid bilayers. The simulations isolate the effect of anion size and show clear differences in the interactions with the dipolar phoshpatidylcholine headgroup. Cl- anions penetrate into the headgroup region of the bilayer, but the simulations confirm theories which predict that larger anions penetrate more deeply, into a more heterogeneous and hydrophobic molecular region. That anion size leads to such differences in partitioning in the bilayer provides atomic-level support to hypotheses inspired by several experimental studies. The ability of larger anions to bury deep within the bilayer is correlated with a less well-structured hydration shell, shedding of which upon penetration incurs a smaller penalty for the larger anions than for Cl-.     

Topological and thermodynamic investigations of molecular interactions in binary mixtures: Molar excess volumes and molar excess enthalpies

Molar excess volumes and molar excess enthalpies of butyl acetate (i) with cyclohexane or benzene or toluene or o-, m- or p-xylene (j) binary mixtures have been measured dilatometrically and calorimetrically over the entire composition range at 308.15 K. The observed data have also been analyzed in terms of graph theoretical approach. The analysis of V^E data by graph theoretical approach suggests that butyl acetate in pure state exists as associated entity and (i + j) mixtures are characterized by the presence of (i–j) molecular entity. It has further been observed that V^E and H^E values calculated by this approach agree well with the corresponding experimental values. The presence of molecular entity is further confirmed by IR study of (i + j) mixture.     

Quantum molecular dynamics study of the reaction of O2 with HOCO

The reaction of O2 with HOCO has been studied by using an ab initio direct dynamics method based on the UB3PW91 density functional theory. Results show that the reaction can occur via two mechanisms: direct hydrogen abstraction and an addition reaction through a short-lived HOC(O)O2 intermediate. The lifetime of the intermediate is predicted to be 660 +/- 30 fs. Although it is an activated reaction, the activation energy is only 0.71 kcal/mol. At room temperature, the obtained thermal rate coefficient is 2.1 x 10(-12) cm3 molecule(-1) s(-1), which is in good agreement with the experimental results.     

Structure and aggregation number of a lyotropic liquid crystal: a fluorescence quenching and molecular dynamics study

The structure and aggregation number of a discotic lyotropic liquid crystal, prepared from tetradecyltrimethylammonium chloride (TDTMACl)/decanol (DeOH)/NaCl/H2O, have been examined using fluorescence quenching of pyrene by hexadecylpyridinium chloride and molecular dynamics (MD). The fluorescence method gives an aggregation number of 258 +/- 25 units (DeOH + TDTMACl). From the MD simulation, a lower limit for the aggregate dimension of 130 units of DeOH + TDTMACl is predicted. A stable oblate aggregate of 240 units was studied in detail. A strong polarization between the ammonium headgroups and chloride ions is observed from the calculated trajectory. DeOH headgroups are located, on average, 0.3 nm more to the interior of the aggregate than the TDTMACl headgroup and contribute to widening the interface by forming H-bonds with water. The radial distribution function of the ammonium headgroup shows that there are 16 water molecules in the first solvation sphere. The diagonal elements of the order parameter tensor of the tail atoms of both surfactants indicate that the interior of the micelle preserves about the same degree of order as at the interface, up to the last three atoms of the aliphatic chain, where the order starts to decrease.     

Theoretical studies on the influence of molecular interactions on the mechanism of electron transfer in photosynthetic reaction center ofRps. viridis

Based on the QM/MM optimized X-ray crystal structure of the photosynthetic reaction center (PRC) of purple bacteriaRhodopseudomonas (Rps.)viridis, quantum chemistry density functional method (DFT, B3LYP/6-31G) has been performed to study the interactions between the pigment molecules and either the surrounded amino acid residues or water molecules that are either axially coordinated or hydrogen bonded with the pigment molecules, leading to an explanation of the mechanism of the primary electron-transfer (ET) reactions in the PRC. Results show that the axial coordination of amino acid residues greatly raises theE _LUMO of pigment molecules and it is important for the possibility of ET to take place. Different hydrogen bonds between amino acid residues, water molecules and pigment molecules decrease theE _LUMO of the pigment molecules to different extents. It is crucial for the ET taking place from excited P along L branch and sustains that the ET is a one-step reaction without through accessory bacteriochlorophyll (ABChl b). It is insufficient to treat the whole protein surrounding as a homogeneous dielectric medium.     

Quantum force molecular dynamics study of the reaction of O atoms with HOCO

The reaction of HOCO with O atoms has been studied using a direct ab initio dynamics approach based on the scaling all correlation UCCD/D95(d,p) method. Ab initio calculations point to two possible reaction mechanisms for the O+HOCO-->OH+CO2 reaction. They are a direct hydrogen abstraction and an oxygen addition reaction through a short-lived HOC(O)O intermediate. The dynamics results show that only the addition mechanism is important under the conditions considered here. The lifetime of the HOC(O)O complex is predicted to be 172+/-15 fs. This is typical of a direct and fast radical-radical reaction. At room temperature, the calculated thermal rate coefficient is 1.44 x 10(-11) cm(3) mol(-1) s(-1) and its temperature dependence is rather weak. The two kinds of reactive trajectories are illustrated in detail.     

Polarization interactions in lattice dynamics of molecular crystals

The contribution to lattice dynamics of molecular crystals of polarization interactions due to dipoles induced by the molecular multipolar field has been evaluated by calculation of the lattice frequencies of crystalline ammonia. It has been found that this contribution is small but not negligible.     

Implementation of pi-pi interactions in molecular dynamics simulation

No explicit pi-pi interaction term has been incorporated in the conventional molecular dynamics (MD) simulation programs in spite of its significant role in the folding of biomolecules and the clustering of organic chemicals. In this article, we propose a technique to emphasize the effect of pi-pi interactions using a function of energy and implement it into an MD simulation program. Several trial calculations show that the pi-pi incorporated program gives improved results consistent with experimental data on atom geometry and has no unfavorable interference with the conventional computational framework. This indicates an importance of the explicit consideration of pi-pi interactions in MD simulation.     

A crossed molecular beam study on the dynamics of F atom reaction with SiH4

In this report, the dynamics of the F+SiH4 reaction has been studied using the universal crossed molecular beam method. Angular resolved time-of-flight spectra have been measured for all reaction products in a single set of experiments. Two different reaction channels have been observed: HF+SiH3 and SiH3F+H. Product angular distributions as well as energy distributions were determined for these two product channels. Experimental results show that the HF product is forward scattered relative to the F atom beam direction, while the SiH3F product is backward scattered relative the F atom beam direction, suggesting that two reaction channels proceed with distinctive reaction dynamics. The relative branching ratios of the two channels have also been estimated.