Investigation of the slide of the single layer of the 1,3,5-triamino-2,4,6-trinitrobenzene crystal: sliding potential and orientation

This paper reports for the first time that the sliding potential of a single layer of the 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) crystal is within 0-77.9 kJ per mol unit cell or 0-29.4 MJ/m(3) and that the most possible sliding orientation is approximately along one line. As compared to another easy-slide material, graphite, TATB has a higher sliding potential and fewer sliding routes and furthermore is more difficult to slide. However, TATB can still slide due to its highest sliding potential points below the apparent activation energy of the decomposition energy of any common explosive. This slide may be the main reason as to why TATB can be used as a desensitizer versus mechanical stimuli.     

Pi-stacked interactions in explosive crystals: buffers against external mechanical stimuli

The pi-stacked interactions in some explosive crystal packing are discussed. Taking a typical pi-stacked explosive 2,4,6-trinitrobenzene-1,3,5-triamine (TATB) as a sample and using molecular simulations, we investigated the nature of the pi-stacked interactions versus the external mechanical stimuli causing possible slide and compression of explosives. As a result, between the neighbor layers in the TATB unit cell, the electrostatic attraction decreases with a little decrease of vdW attraction when its top layer slides, whereas the vdW attraction increases with a decrease of electrostatic attraction when TATB crystal is compressed along its c axis. Meanwhile, we studied the correlation between the pi-stacked structures and the impact sensitivities of explosives by means of three representatives including TATB with typical planar pi-stacked structures, 2,2-dinitroethylene-1,1-diamine (Fox-7) with wavelike pi-stacked structures, and 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) without pi-stacked structure. The results showed that pi-stacked structures, particularly planar layers, can effectively buffer against external mechanical stimuli. That is, pi-stacked structures can partly convert the mechanical energy acting on them into their intermolecular interaction energy, to avoid the increase of the molecular vibration resulting in the explosive decomposition, the formation of hot spots, and the final detonation. This is another reason for the low mechanical sensitivity of pi-stacked explosives besides their stable conjugated molecular structures.     

Conformational dependence of charges in protein simulations

We have studied the conformational dependence of molecular mechanics atomic charges for proteins by calculating the charges fitted to the quantum mechanical (QM) electrostatic potential (ESP) for all atoms in complexes between avidin and seven biotin analogues for 20 snapshots from molecular dynamics simulations. We have studied how various other charge sets reproduce those charges. The QM charges, even if averaged over all snapshots or all residues, in general have a larger magnitude than standard Amber charges, indicating that the restraint toward zero in the restrained ESP method is too strong. This has a significant influence on the electrostatic conformational energies and the interaction energy between the biotin ligand and the protein, giving a difference between the QM and Amber charges of 43 and 8 kJ/mol for the negatively charged and neutral biotin analogues, respectively (3-4%). However, this energy difference is strongly reduced if the solvation energy (calculated by the Poisson-Boltzmann or Generalized Born methods) is added, viz., to 7 kJ/mol for charged and 3 kJ/mol for uncharged ligand. In fact, charges need to be recalculated with a QM method only for residues within 7 or 4 A of the ligand, if the error should be less than 4 kJ/mol. Unfortunately, the QM charges do not give significantly better MM/PBSA estimates of ligand-binding affinities than standard Amber charges.     

Theoretical Investigation on Mechanism,Thermochemistry, and Kinetics of the Gas-phase Reaction of 2-Propargyl Radical with Formaldehyde

Gas-phase mechanism and kinetics of the reactions of the 2-propargyl radical(H2CCCH), an important intermediate in combustion processes, with formaldehyde were investigated using ab initio molecular orbital theory at the coupled-cluster CCSD(T)//B3LYP/6-311++G(3df,2p) method in conjunction with transition state theory(TST), variational transition state theory(VTST) and Rice-Ramsperger-Kassel-Marcus(RRKM) calculations for rate constants. The potential energy surface(PES) constructed shows that the H2CCCH+HCHO reaction has six main entrances, including two H-abstraction and four additional channels, in which the former is energetically more favorable. The H-abstraction channels slide down to two quite weak pre-complexes COM-01(-9.3 kJ/mol) and COM-02(-kJ/mol) before going via energy barriers of 71.3(T0/P1) and 63.9 kJ/mol(T0/P2), respectively. Two post-complexes, COM-1(-17.8 kJ/mol) and COM-2(-23.4 kJ/mol) created just after coming out from T0/P1 and T0/P2, respectively, can easily be decomposed via barrier-less processes yielding H2CCCH2+CHO(P1,-12.4 kJ/mol) and HCCCH3+CHO(P2,-16.5 kJ/mol), respectively. The additional channels occur initially by formation of four intermediate states, H2CCCHCH2O(I1, 1.1 kJ/mol), HCCCH2CH2O(I3, 4.5 kJ/mol), H2CCCHOCH2(I4, 10.2 kJ/mol), and HCCCH2OCH2(I6, 19.1 kJ/mol) via energy barriers of 66.3, 59.2, 112.2, and 98.6 kJ/mol at T0/1, T0/3, TOM, and TO/6, respectively. Of which two channels producing 14 and 16 can be ignored due to coming over tlie high barriers TOM and TO/6, respectively. The rate constants and product branching ratios for the low-energy channels calculated show that the H2CCCH+HCHO reaction is almost pressure-independent. Altliough the H2CCCH+HCHO→Ⅰ1 and H2CCCH+HCHO→Ⅰ3 channels become dominant at low temperature, however, they are less competitive channels at high temperature.     

Modeling water exchange on an aluminum polyoxocation

For the first time, water exchange on a polymeric complex has been modeled using a combination of gas-phase ab initio calculations and molecular dynamics (MD) simulations. The GaO4Al12(OH)24(H2O)12(7+)aq ion (GaAl12) was chosen because high-quality experimental data exist, including an activation enthalpy (+63 +/- 7 kJ/mol) and an activation volume (+3 +/- 1 cm3/mol). We took a two-step approach. First, the local solvent structure and the initial states for reaction were inferred from the molecular dynamics simulations. Second, we used this information to evaluate initial-state structures in the ab initio calculations. The energy differences between the initial and transition states from the ab initio calculations varied from +59 kJ/mol to +53 kJ/mol depending upon details, closely approximating the activation enthalpy.     

多巴胺在其第三受体蛋白结构中的分子通道上传输动力学

本文基于多巴胺与其第三受体复合蛋白(D_3R)结构,采用分子动力学技术Gromacs 4.5程序中的伞形样本方法,研究多巴胺在多巴胺第三受体蛋白结构中的运动轨迹及其过程中自由能变化,探讨多巴胺在其分子通道上传输运动机制动力学。分子模拟表明,处在发挥神经递质作用部位的多巴胺,通过D_3R结构中的功能分子通道沿着y+轴朝细胞外方向传输运动的自由能变化数值为134.6 kJ?mol~(-1),沿着y-轴朝细胞内传输运动的自由能变化为211.5 kJ?mol~(-1)。在D_3R结构中,多巴胺沿着x+、x-、z+、z-轴朝细胞双层膜方向传输运动的自由能变化分别为65.8、245.0、551.4、172.8 kJ?mol~(-1),数值说明DOP更容易沿着x+轴方向从TM5(第五跨膜螺旋)与TM6(第六跨膜螺旋)缝隙之间离开D_3R内部结构。处在细胞间隙空间的自由多巴胺,在等温等压条件下沿着逆y+轴方向通过多巴胺第三受体内功能分子通道,到达发挥神经递质作用的部位是一个自发过程,因为在该轨迹上多巴胺分子与受体相互作用是一个负自由能变化(-134.6 kJ?mol~(-1))。所以,多巴胺与多巴胺受体很容易相互结合,发挥神经递质作用。发挥了神经递质功能作用的多巴胺分子,沿着x+轴方向的保护分子通道从TM5与TM6缝隙之间离开D_3R内部结构,避免过度发挥多巴胺神经递质功能作用。根据多巴胺功能和保护分子通道观点,我们提出帕金森病新病理和精神分裂症新病理。论文还探讨多巴胺分子通道理论及其新病理应用于治疗控制这两种病症及其相关药物研究开发。     

Characterization of tunneling systems in molecular versus polymer glasses by high-pressure photon echo spectroscopy

Intrinsic differences between tunneling two-level systems (TLSs) in molecular versus polymeric glasses are revealed by studying the effect of compression on TLS dynamics. Photon echo studies under variable low-temperature (1.1-2.3 K) and high-pressure (0-30 kbar) conditions have been performed to contrast the effect of compression on molecular [2-methyl-tetrahydrofuran (2MTHF)] versus polymer [Polymethylmethacrylate (PMMA)] glasses. The pressure-induced reduction in the magnitude of the optical dephasing rate of rhodamine 640 in a molecular glass (2MTHF) is found to be comparable to the volume decrease of the glass (e.g., approximately 20% at 30 kbar), indicating that TLSs in 2MTHF are associated with void space or low-density regions of the glass. In contrast, the relative pressure insensitivity observed for organic polymer glasses (PMMA) supports the idea that these TLSs are associated with side chain defects. The power-law exponent for the temperature-dependent dephasing in 2MTHF also decreased significantly at high pressure, suggesting a change in the form of the TLS density of states upon compression of the molecular glass.     

Vibrational spectroscopic determination of local solvent electric field, solute-solvent electrostatic interaction energy, and their fluctuation amplitudes

IR probes have been extensively used to monitor local electrostatic and solvation dynamics. Particularly, their vibrational frequencies are highly sensitive to local solvent electric field around an IR probe. Here, we show that the experimentally measured vibrational frequency shifts can be inversely used to determine local electric potential distribution and solute-solvent electrostatic interaction energy. In addition, the upper limits of their fluctuation amplitudes are estimated by using the vibrational bandwidths. Applying this method to fully deuterated N-methylacetamide (NMA) in D(2)O and examining the solvatochromic effects on the amide I' and II' mode frequencies, we found that the solvent electric potential difference between O(═C) and D(-N) atoms of the peptide bond is about 5.4 V, and thus, the approximate solvent electric field produced by surrounding water molecules on the NMA is 172 MV/cm on average if the molecular geometry is taken into account. The solute-solvent electrostatic interaction energy is estimated to be -137 kJ/mol, by considering electric dipole-electric field interaction. Furthermore, their root-mean-square fluctuation amplitudes are as large as 1.6 V, 52 MV/cm, and 41 kJ/mol, respectively. We found that the water electric potential on a peptide bond is spatially nonhomogeneous and that the fluctuation in the electrostatic peptide-water interaction energy is about 10 times larger than the thermal energy at room temperature. This indicates that the peptide-solvent interactions are indeed important for the activation of chemical reactions in aqueous solution.     

Calculations on the competition between association and reaction for C3H(+) + H2

A potential energy surface has been calculated for the competing associative and reactive ion-molecule processes involving the reactants C3H(+) + H2. Our ab initio results show that the linear ion C3H+ and H2 can directly access the deep potential well of the propargyl ion H2CCCH+, which is calculated to lie 390 kJ mol-1 below the zero-point energy of the reactants. Isomerization between the propargyl ion and the lower energy, cyclic C3H3+ ion, calculated to lie 501 kJ mol-1 below the zero-point energy of reactants, can subsequently occur via two pathways. One of these pathways involves a transition state lying 22 kJ mol-1 below the energy of the reactants while the other, which occurs at much lower energies, involves two transition states and an intermediate. The dissociation of c-C3H3+ into c-C3H2(+) + H is calculated to occur directly, without any intermediate potential energy maximum, but the energy of the products lies 7.3 kJ mol-1 above the energy of the reactants. Using the minimum energy potential pathway and properties of the stationary point structures determined via ab initio methods, we have calculated both the association rate coefficient to produce C3H3+ as a function of density and the branching ratio between the propargyl and cyclic structures of the ion. Our results are in good agreement with some experimental results and in conflict with others. Specifically, we agree with the 1:1 branching ratio measured for the propargyl and cyclic isomers of C3H3+ at 80 and 300 K and we agree with the rate coefficient for radiative association measured at 80 K. We cannot reproduce reported measurements that the reactive channel (C3H2(+) + H) is the dominant channel at 80 K and at low gas densities, or that the association channel at high densities saturates at an effective rate coefficient well below the Langevin value -2x10(-11) cm3 s-1 at 300K and 1x10(-10) cm3 s-1 at 80K.     

Predicted thermochemistry and unimolecular kinetics of nitrous sulfide

The geometry of N(2)S was obtained at the CCSD(T)/aug-cc-pV(T + d)Z level of theory and energies with coupled-cluster single double triple (CCSD(T)) and basis sets up to aug-cc-pV(6 + d)Z. After correction for anharmonic zero-point energy, core-valence correlation, correlation up to CCSDT(Q) and relativistic effects, D(0) for the N-S bond is estimated as 71.9 kJ mol(-1), and the corresponding thermochemistry for N(2)S is Δ(f)H(0)(°)=205.4 kJ mol(-1) and Δ(f)H(298)(°)=202.6 kJ mol(-1) with an uncertainty of ±2.5 kJ mol(-1). Using CCSD(T)/aug-cc-pV(T + d) theory the minimum energy crossing point between singlet and triplet potential energy curves is found at r(N-N) ≈ 1.105 ? and r(N-S) ≈ 2.232 ?, with an energy 72 kJ mol(-1) above N(2) + S((3)P). Application of Troe's unimolecular formalism yields the low-pressure-limiting rate constant for dissociation of N(2)S k(0) = 7.6 × 10(-10) exp(-126 kJ mol(-1)/RT) cm(3) molecule(-1) s(-1) over 700-2000 K. The estimated uncertainty is a factor of 4 arising from unknown parameters for energy transfer between N(2)S and Ar or N(2) bath gas. The thermochemistry and kinetics were included in a mechanism for CO/H(2)/H(2)S oxidation and the conclusion is that little NO is produced via subsequent chemistry of NNS.     

QM/MM-PBSA method to estimate free energies for reactions in proteins

We have developed a method to estimate free energies of reactions in proteins, called QM/MM-PBSA. It estimates the internal energy of the reactive site by quantum mechanical (QM) calculations, whereas bonded, electrostatic, and van der Waals interactions with the surrounding protein are calculated at the molecular mechanics (MM) level. The electrostatic part of the solvation energy of the reactant and the product is estimated by solving the Poisson-Boltzmann (PB) equation, and the nonpolar part of the solvation energy is estimated from the change in solvent-accessible surface area (SA). Finally, the change in entropy is estimated from the vibrational frequencies. We test this method for five proton-transfer reactions in the active sites of [Ni,Fe] hydrogenase and copper nitrite reductase. We show that QM/MM-PBSA reproduces the results of a strict QM/MM free-energy perturbation method with a mean absolute deviation (MAD) of 8-10 kJ/mol if snapshots from molecular dynamics simulations are used and 4-14 kJ/mol if a single QM/MM structure is used. This is appreciably better than the original QM/MM results or if the QM energies are supplemented with a point-charge model, a self-consistent reaction field, or a PB model of the protein and the solvent, which give MADs of 22-36 kJ/mol for the same test set.     

Dynamics of structure and energy of horse carboxymyoglobin after photodissociation of carbon monoxide.

The energetics and structural volume changes after photodissociation of carboxymyoglobin are quantitatively investigated by laser-induced transient grating (TG) and photoacoustic calorimetric techniques. Various origins of the TG signal are distinguished: the phase grating signals due to temperature change, due to absorption spectrum change, and due to volume change. We found a new kinetics of approximately 700 ns (at room temperature), which was not observed by the flash photolysis technique. This kinetics should be attributed to the intermediate between the geminate pair and the fully dissociated state. The enthalpy of an intermediate species is determined to be 61 +/- 10 kJ/mol, which is smaller than the expected Fe-CO bond energy. The volume of MbCO slightly contracts (5 +/- 3 cm(3)/mol) during this process. CO is fully released from the protein by an exponential kinetics from 25 to -2 degrees C. During this escaping process, the volume expands by 14.7 +/- 2 cm(3)/mol at room temperature and 14 +/- 10 kJ/mol is released, which should represent the protein relaxation and the solvation of the CO (the enthalpy of this final state is 47 +/- 10 kJ/mol). A potential barrier between the intermediate and the fully dissociated state is DeltaH(*) = 41.3 kJ/mol and DeltaS(*) = 13.6 J mol(-1) K(-1). The TG experiment under a high wavenumber reveals that the volume expansion depends on the temperature from 25 to -2 degrees C. The volume changes and the energies of the intermediate species are discussed.     

A crossed molecular beams and ab initio study on the formation of C6H3 radicals. an interface between resonantly stabilized and aromatic radicals

The crossed molecular beams reaction of dicarbon molecules, C(2)(X(1)Σ(g)(+)/a(3)Π(u)) with vinylacetylene was studied under single collision conditions at a collision energy of 31.0 kJ mol(-1) and combined with electronic structure calculations on the singlet and triplet C(6)H(4) potential energy surfaces. The investigations indicate that both reactions on the triplet and singlet surfaces are dictated by a barrierless addition of the dicarbon unit to the vinylacetylene molecule and hence indirect scattering dynamics via long-lived C(6)H(4) complexes. On the singlet surface, ethynylbutatriene and vinyldiacetylene were found to decompose via atomic hydrogen loss involving loose exit transition states to form exclusively the resonantly stabilized 1-hexene-3,4-diynyl-2 radical (C(6)H(3); H(2)CCCCCCH; C(2v)). On the triplet surface, ethynylbutatriene emitted a hydrogen atom through a tight exit transition state located about 20 kJ mol(-1) above the separated stabilized 1-hexene-3,4-diynyl-2 radical plus atomic hydrogen product; to a minor amount (<5%) theory predicts that the aromatic 1,2,3-tridehydrobenzene molecule is formed. Compared to previous crossed beams and theoretical investigations on the formation of aromatic C(6)H(x) (x = 6, 5, 4) molecules benzene, phenyl, and o-benzyne, the decreasing energy difference from benzene via phenyl and o-benzyne between the aromatic and acyclic reaction products, i.e., 253, 218, and 58 kJ mol(-1), is narrowed down to only ～7 kJ mol(-1) for the C(6)H(3) system (aromatic 1,2,3-tridehydrobenzene versus the resonantly stabilized free radical 1-hexene-3,4-diynyl-2). Therefore, the C(6)H(3) system can be seen as a "transition" stage among the C(6)H(x) (x = 6-1) systems, in which the energy gap between the aromatic isomer (x = 6, 5, 4) is reduced compared to the acyclic isomer as the carbon-to-hydrogen ratio increases and the acyclic isomer becomes more stable (x = 1, 2).     

Photodissociation dynamics of acetoxime in gas phase

The dynamics of photodissociation of acetoxime at 193 nm, leading to the formation of (CH3)2C=N and OH fragments, has been investigated. The nascent OH radicals, which are both rotationally and vibrationally excited, were probed by laser photolysis-laser induced fluorescence technique. OH fragments in both v" = 1 and v" = 0 vibrational states were detected with a ratio of population in the higher to lower level of 0.07+/-0.01. The rotational temperatures of v" = 0 and 1 levels of OH radicals are 2650+/-150 K and 1290+/-20 K, respectively. More than 30% of the available energy, i.e., 115+/-21 kJ mol(-1) is partitioned into the relative translational energy of the fragments. The results of excited electronic state and transition state calculations at the configuration interaction with single electronic excitation level suggest that the dissociation takes place with an exit barrier of approximately 126 kJ mol(-1) at the triplet state (T2) potential energy surface, formed by internal conversions/intersystem crossing from the initially populated S2 state. Using the calculated transition state geometry and its energy, the observed energy distribution pattern can be reproduced by the hybrid model within experimental uncertainties. The presence of an exit barrier is further supported by the observation of N-OH dissociation upon 248 nm excitation, where the relative translational energy of the fragments is found to be approximately 96 kJ mol(-1). The photodissociation dynamics of acetoxime is compared with C-OH dissociation in enols and carboxylic acid and N-OH dissociation in nitrous acid. The observed emission (lambda(max)=430 nm) and the N-OH dissociation dynamics indicate crossing of the initially populated state to an emissive state of acetoxime, which is different from the dissociative state.     

Anion conformation of low-viscosity room-temperature ionic liquid 1-ethyl-3-methylimidazolium bis(fluorosulfonyl) imide

Anion conformation of a low-viscosity room-temperature ionic liquid 1-ethyl-3-methylimidazolium bis(fluorosulfonyl) imide (EMI+FSI-) has been studied by Raman spectra and theoretical DFT calculations. Three strong Raman bands were found at 293, 328, and 360 cm(-1), which are ascribed to the FSI- ion. These Raman bands show significant temperature dependence, implying that two FSI- conformers coexist in equilibrium. This is supported by theoretical calculations that the FSI- ion is present as either C2 (trans) or C1 (cis) conformer; the former gives the global minimum, and the latter has a higher SCF energy of about 4 kJ mol(-1). Full geometry optimizations followed by normal frequency analyses show that the observed bands at 293, 328, and 360 cm(-1) are ascribed to the C2 conformer. The corresponding vibrations at 305, 320, and 353 cm(-1) were extracted according to deconvolution of the observed Raman bands in the range280-400 cm(-1 )and are ascribed to the C1 conformer. The enthalpy DeltaH degrees of conformational change from C2 to C1 was experimentally evaluated to be ca. 4.5 kJ mol(-1), which is in good agreement with the predicted value by theoretical calculations. The bis(trifluoromethanesulfonyl) imide anion (TFSI-) shows a conformational equilibrium between C1 and C2 analogues (DeltaH degrees = 3.5 kJ mol(-1)). However, the profile of the potential energy surface of the conformational change for FSI- (the F-S-N-S dihedral angle) is significantly different from that for TFSI- (the C-S-N-S dihedral angle).     

Adsorption dynamics of water on Pt{110}-(1 x 2)

The dynamics of H(2)O adsorption on Pt{110}-(1 x 2) is studied using supersonic molecular beam and temperature programed desorption techniques. The sticking probabilities are measured using the King and Wells method at a surface temperature of 165 K. The absolute initial sticking probability s(0) of H(2)O is 0.54+/-0.03 for an incident kinetic energy of 27 kJmol. However, an unusual molecular beam flux dependence on s(0) is also found. At low water coverage (theta<1), the sticking probability is independent of coverage due either to diffusion in an extrinsic precursor state formed above bilayer islands or to incorporation into the islands. We define theta=1 as the water coverage when the dissociative sticking probability of D(2) on a surface predosed with water has dropped to zero. The slow falling H(2)O sticking probability at theta>1 results from compression of the bilayer and the formation of multilayers. Temperature programed desorption of water shows fractional order kinetics consistent with hydrogen-bonded islands on the surface. A remarkable dependence of the initial sticking probability on the translational (1-27 kJ/mol) and internal energies of water is observed: s(0) is found to be essentially a step function of translational energy, increasing fivefold at a threshold energy of 5 kJ/mol. The threshold migrates to higher energies with increasing nozzle temperature (300-700 K). We conclude that both rotational state and rotational alignment of the water molecules in the seeded supersonic expansion are implicated in dictating the adsorption process.     

Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations

Combined ab initio quantum mechanical and molecular mechanical calculations have been widely used for modeling chemical reactions in complex systems such as enzymes, with most applications being based on the determination of a minimum energy path connecting the reactant through the transition state to the product in the enzyme environment. However, statistical mechanics sampling and reaction dynamics calculations with a combined ab initio quantum mechanical (QM) and molecular mechanical (MM) potential are still not feasible because of the computational costs associated mainly with the ab initio quantum mechanical calculations for the QM subsystem. To address this issue, a reaction path potential energy surface is developed here for statistical mechanics and dynamics simulation of chemical reactions in enzymes and other complex systems. The reaction path potential follows the ideas from the reaction path Hamiltonian of Miller, Handy and Adams for gas phase chemical reactions but is designed specifically for large systems that are described with combined ab initio quantum mechanical and molecular mechanical methods. The reaction path potential is an analytical energy expression of the combined quantum mechanical and molecular mechanical potential energy along the minimum energy path. An expansion around the minimum energy path is made in both the nuclear and the electronic degrees of freedom for the QM subsystem internal energy, while the energy of the subsystem described with MM remains unchanged from that in the combined quantum mechanical and molecular mechanical expression and the electrostatic interaction between the QM and MM subsystems is described as the interaction of the MM charges with the QM charges. The QM charges are polarizable in response to the changes in both the MM and the QM degrees of freedom through a new response kernel developed in the present work. The input data for constructing the reaction path potential are energies, vibrational frequencies, and electron density response properties of the QM subsystem along the minimum energy path, all of which can be obtained from the combined quantum mechanical and molecular mechanical calculations. Once constructed, it costs much less for its evaluation. Thus, the reaction path potential provides a potential energy surface for rigorous statistical mechanics and reaction dynamics calculations of complex systems. As an example, the method is applied to the statistical mechanical calculations for the potential of mean force of the chemical reaction in triosephosphate isomerase.     

TGA application for optimising the accelerated aging conditions and predictions of thermal aging of rubber

Changes in the residual compression set, tensile strength and elongation at break, as well as the oxygen absorption and mass change, are evaluated during the thermal oxidation of butadiene-nitrile-based carbon black-filled rubber. Activation energies for the processes are determined. Using TGA, the activation energy of the first thermal degradation stage (87-88 kJ/mol) corresponded to the increase in compression set. The activation energy of the second stage (116-117 kJ/mol) corresponded to the decrease in the elongation at break and oxygen absorption. These correlations confirm that TGA can be used to predict the thermal stability of rubber.     

The opsin shift and mechanism of spectral tuning in rhodopsin

Molecular dynamics simulations and combined quantum mechanical and molecular mechanical calculations have been performed to investigate the mechanism of the opsin shift and spectral tuning in rhodopsin. A red shift of -980 cm(-1) was estimated in the transfer of the chromophore from methanol solution environment to the protonated Schiff base (PSB)-binding site of the opsin. The conformational change from a 6-s-cis-all-trans configuration in solution to the 6-s-cis-11-cis conformer contributes additional -200 cm(-1), and the remaining effects were attributed to dispersion interactions with the aromatic residues in the binding site. An opsin shift of 2100 cm(-1) was obtained, in reasonable accord with experiment (2730 cm(-1)). Dynamics simulations revealed that the 6-s-cis bond can occupy two main conformations for the β-ionone ring, resulting in a weighted average dihedral angle of about -50°, which may be compared with the experimental estimate of -28° from solid-state NMR and Raman data. We investigated a series of four single mutations, including E113D, A292S, T118A, and A269T, which are located near the PSB, along the polyene chain of retinal and close to the ionone ring. The computational results on absorption energy shift provided insights into the mechanism of spectral tuning, which involves all means of electronic structural effects, including the stabilization or destabilization of either the ground or the electronically excited state of the retinal PSB.     

Modeling of phase equilibrium and vapor adsorption on carbon black based on a combination of a lattice theory and equation of state

A thermodynamic approach is developed in this paper to describe the behavior of a subcritical fluid in the neighborhood of vapor-liquid interface and close to a graphite surface. The fluid is modeled as a system of parallel molecular layers. The Helmholtz free energy of the fluid is expressed as the sum of the intrinsic Helmholtz free energies of separate layers and the potential energy of their mutual interactions calculated by the 10-4 potential. This Helmholtz free energy is described by an equation of state (such as the Bender or Peng-Robinson equation), which allows us a convenient means to obtain the intrinsic Helmholtz free energy of each molecular layer as a function of its two-dimensional density. All molecular layers of the bulk fluid are in mechanical equilibrium corresponding to the minimum of the total potential energy. In the case of adsorption the external potential exerted by the graphite layers is added to the free energy. The state of the interface zone between the liquid and the vapor phases or the state of the adsorbed phase is determined by the minimum of the grand potential. In the case of phase equilibrium the approach leads to the distribution of density and pressure over the transition zone. The interrelation between the collision diameter and the potential well depth was determined by the surface tension. It was shown that the distance between neighboring molecular layers substantially changes in the vapor-liquid transition zone and in the adsorbed phase with loading. The approach is considered in this paper for the case of adsorption of argon and nitrogen on carbon black. In both cases an excellent agreement with the experimental data was achieved without additional assumptions and fitting parameters, except for the fluid-solid potential well depth. The approach has far-reaching consequences and can be readily extended to the model of adsorption in slit pores of carbonaceous materials and to the analysis of multicomponent adsorption systems.