Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces.

In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface. The simulations reveal how this energy transfer depends on the collision energy, incident angle, biological ion, and surface. With energy transfer to the ion's vibration fragmentation may occur, i.e. surface-induced dissociation (SID), and the simulations discovered a new fragmentation mechanism, called shattering, for which the ion fragments as it collides with the surface. The simulations also provide insight into the atomistic dynamics of soft-landing and reactive-landing of ions on surfaces. The CID simulations compared activation by multiple "soft" collisions, resulting in random excitation, versus high energy single collisions and nonrandom excitation. These two activation methods may result in different fragment ions. Simulations provide fragmentation products in agreement with experiments and, hence, can provide additional information regarding the reaction mechanisms taking place in experiment. Such studies paved the way on using simulations as an independent and predictive tool in increasing fundamental understanding of CID and related processes.

Organic sensitizers featuring a planar indeno[1,2-b]-thiophene for efficient dye-sensitized solar cells.

An efficient organic sensitizer (JK-306) featuring a planar indeno[1,2-b]thiophene as the π-linker of a bridging unit for dye-sensitized solar cells (DSSCs) was synthesized. The sensitizer had a strong molar absorption coefficient and a red-shifted absorption band compared with JK-305, which resulted in a significant increase in the short-circuit photocurrent density. We incorporated a highly congested bulky amino group into the 2',4'-dihexyloxybiphenyl-4-yl moiety, an electron donor, to diminish the charge recombination and to prevent aggregation of the sensitizer. Under standard AM 1.5G solar conditions, JK-306-sensitized cells in the presence of co-adsorbents chenodeoxycholic acid (CDCA) and 4-[bis(9,9-dimethyl-9H-fluoren-2-yl)amino]benzoic acid (HC-A), which afforded an overall conversion efficiency of 8.37% and 8.52%, respectively. Upon changing the I(-) /I3 (-) electrolyte to the Co(II) /Co(III) redox couple, the cell gave rise to a significantly improved conversion efficiency of 10.02% with the multifunctional HC-A, which is one of the highest values reported for DSSCs with a cobalt-based electrolyte. Furthermore, the JK-306-based solar cell with a polymer gel electrolyte revealed a high conversion efficiency of 7.61%, which is one of the highest values for cells based on organic sensitizers.

Electron-rich anthracene semiconductors containing triarylamine for solution-processed small-molecule organic solar cells.

New electron-rich anthracene derivatives containing triarylamine hole stabilizers, 2,6-bis[5,5'-bis(N,N'-diphenylaniline)-2,2'-bithiophen-5-yl]-9,10-bis-[(triisopropylsilyl)ethynyl]anthracene (TIPSAntBT-TPA) and 2,6-bis(5,5'-bis{4-[bis(9,9-dimethyl-9H-fluoren-2-yl)amino]phenyl}-2,2'-bithiophen-5-yl)-9,10-bis-[(triisopropylsilyl)ethynyl]anthracene (TIPSAntBT-bisDMFA), linked with π-conjugated bithiophene bridges, were synthesized and their photovoltaic characteristics were investigated in solution-processed small-molecule organic solar cells (SMOSCs). These new materials exhibited superior intramolecular charge transfer from triarylamine to anthracene, leading to a more electron-rich anthracene core that facilitated electron transfer into phenyl-C(61)-butyric acid methyl ester. Compared with TIPSAntBT and triarylamine, these materials show a threefold improvement in hole-transporting properties and better photovoltaic performance in solution-processed SMOSCs, with the best power conversion efficiency being 2.96 % at a high open-circuit voltage of 0.85 V.

Facile synthesis of fluorine-substituted benzothiadiazole-based organic semiconductors and their use in solution-processed small-molecule organic solar cells.

A facile new protocol for the synthesis of iodinated derivatives of fluorinated benzothiadiazoles is demonstrated for the production of p-type semiconducting materials. The newly synthesized small-molecule compounds bis[TPA-diTh]-MonoF-BT and bis[TPA-diTh]-DiF-BT exhibited a power conversion efficiency of 2.95% and a high open-circuit voltage of 0.85 V in solution-processed small-molecule organic solar cells.

Collision induced dissociation of doubly-charged ions: Coulomb explosion vs. neutral loss in [Ca(urea)]2+ gas phase unimolecular reactivity via chemical dynamics simulations.

In this paper we report different theoretical approaches to study the gas-phase unimolecular dissociation of the doubly-charged cation [Ca(urea)](2+), in order to rationalize recent experimental findings. Quantum mechanical plus molecular mechanical (QM/MM) direct chemical dynamics simulations were used to investigate collision induced dissociation (CID) and rotational-vibrational energy transfer for Ar + [Ca(urea)](2+) collisions. For the picosecond time-domain of the simulations, both neutral loss and Coulomb explosion reactions were found and the differences in their mechanisms elucidated. The loss of neutral urea subsequent to collision with Ar occurs via a shattering mechanism, while the formation of two singly-charged cations follows statistical (or almost statistical) dynamics. Vibrational-rotational energy transfer efficiencies obtained for trajectories that do not dissociate during the trajectory integration were used in conjunction with RRKM rate constants to approximate dissociation pathways assuming complete intramolecular vibrational energy redistribution (IVR) and statistical dynamics. This statistical limit predicts, as expected, that at long time the most stable species on the potential energy surface (PES) dominate. These results, coupled with experimental CID from which both neutral loss and Coulomb explosion products were obtained, show that the gas phase dissociation of this ion occurs by multiple mechanisms leading to different products and that reactivity on the complicated PES is dynamically complex.

New type of organic sensitizers with a planar amine unit for efficient dye-sensitized solar cells.

A new type of organic sensitizers incorporating a planar amine unit have been synthesized and demonstrated to be a highly efficient sensitizers, showing evidence of lateral interactions on the TiO(2) surface. Under standard global air mass 1.5 solar conditions, the JK-98 sensitized cell gave a short circuit photocurrent density (J(sc)) of 16.78 mA cm(-2), an open-circuit voltage (V(oc)) of 0.745 V, and a fill factor (ff) of 0.70, corresponding to an overall conversion efficiency (η) of 8.71%.

Mechanism and kinetics of the reaction NO3 + C2H4.

The reaction of NO(3) radical with C(2)H(4) was characterized using the B3LYP, MP2, B97-1, CCSD(T), and CBS-QB3 methods in combination with various basis sets, followed by statistical kinetic analyses and direct dynamics trajectory calculations to predict product distributions and thermal rate constants. The results show that the first step of the reaction is electrophilic addition of an O atom from NO(3) to an olefinic C atom from C(2)H(4) to form an open-chain adduct. A concerted addition reaction mechanism forming a five-membered ring intermediate was investigated, but is not supported by the highly accurate CCSD(T) level of theory. Master-equation calculations for tropospheric conditions predict that the collisionally stabilized NO(3)-C(2)H(4) free-radical adduct constitutes 80-90% of the reaction yield and the remaining products consist mostly of NO(2) and oxirane; the other products are produced in very minor yields. By empirically reducing the barrier height for the initial addition step by 1 kcal mol(-1) from that predicted at the CBS-QB3 level of theory and treating the torsional modes explicitly as one-dimensional hindered internal rotations (instead of harmonic oscillators), the computed thermal rate constants (including quantum tunneling) can be brought into very good agreement with the experimental data for the overall reaction rate constant.

Efficient and stable panchromatic squaraine dyes for dye-sensitized solar cells.

A new series of stable, unsymmetrical squaraine near-IR sensitizers (JK-216 and JK-217), which are assembled using both thiophenyl pyrrolyl and indolium groups, exhibit a panchromatic light harvesting up to 780 nm. The JK-216 based cell exhibited a record efficiency of 6.29% for near-IR DSSCs. In addition, the JK-217 device showed an excellent stability under a light soaking test at 60 °C for 1000 h.

High molar extinction coefficient organic sensitizers for efficient dye-sensitized solar cells.

We have designed and synthesized highly efficient organic sensitizers with a planar thienothiophene-vinylene-thienothiophene linker. Under standard global AM 1.5 solar conditions, the JK-113-sensitized cell gave a short circuit photocurrent density (J(sc)) of 17.61 mA cm(-2), an open-circuit voltage (V(oc)) of 0.71 V, and a fill factor (FF) of 72%, corresponding to an overall conversion efficiency (eta) of 9.1%. The incident monochromatic photo-to-current conversion efficiency (IPCE) of JK-113 exceeds 80% over the spectral region from 400 to 640 nm, reaching its maximum of 93% at 475 nm. The band tails off toward 770 nm, contributing to the broad spectral light harvesting. Solar-cell devices based on the sensitizer JK-113 in conjunction with a volatile electrolyte and a solvent-free ionic liquid electrolyte gave high conversion efficiencies of 9.1% and 7.9%, respectively. The JK-113-based solar cell fabricated using a solvent-free ionic liquid electrolyte showed excellent stability under light soaking at 60 degrees C for 1000 h.

Protonated urea collision-induced dissociation. Comparison of experiments and chemical dynamics simulations.

Quantum mechanical plus molecular mechanical direct chemical dynamics were used, with electrospray tandem mass spectrometry experiments, potential energy surface calculations, and RRKM analyses, to study the gas-phase collision-induced dissociation (CID) of protonated urea. The direct dynamics were able to reproduce some of the experimental observations, in particular the presence of two fragmentation pathways, and, thus, to explain the dynamical origin of the two fragmentation ions observed in the CID spectra. A shattering dissociation mechanism takes place during the collision, and it becomes more important as the collision energy increases, thus explaining the linear increase of the high-energy reaction path (loss of ammonia) versus collision energy. By combining the different theoretical and experimental findings, a complete dynamical picture leading to the fragmentation was identified: (i) Oxygen-protonated urea, the most stable structure in the gas phase, must first isomerize to the nitrogen-protonated form. This can happen by multiple CID collisions or in the electrospray ionization process. (ii) Once the nitrogen-protonated isomer is formed, it can dissociate via two mechanisms: i.e, a slow, almost statistical, process forming a NH(4)(+)--NHCO intermediate that rapidly dissociates or a fast nonstatistical process which may lead to the high-energy products.

Importance of shattering fragmentation in the surface-induced dissociation of protonated octaglycine.

A QM + MM direct chemical dynamics simulation was performed to study collisions of protonated octaglycine, gly(8)-H(+), with the diamond {111} surface at an initial collision energy E(i) of 100 eV and incident angle theta(i) of 0 degrees and 45 degrees. The semiempirical model AM1 was used for the gly(8)-H(+) intramolecular potential, so that its fragmentation could be studied. Shattering dominates gly(8)-H(+) fragmentation at theta(i) = 0 degrees, with 78% of the ions dissociating in this way. At theta(i) = 45 degrees shattering is much less important. For theta(i) = 0 degrees there are 304 different pathways, many related by their backbone cleavage patterns. For the theta(i) = 0 degrees fragmentations, 59% resulted from both a-x and b-y cleavages, while for theta(i) = 45 degrees 70% of the fragmentations occurred with only a-x cleavage. For theta(i) = 0 degrees, the average percentage energy transfers to the internal degrees of freedom of the ion and the surface, and the energy remaining in ion translation are 45%, 26%, and 29%. For 45 degrees these percentages are 26%, 12%, and 62%. The percentage energy-transfer to DeltaE(int) for theta(i) = 0 degrees is larger than that reported in previous experiments for collisions of des-Arg(1)-bradykinin with a diamond surface at the same theta(i). This difference is discussed in terms of differences between the model diamond surface used in the simulations and the diamond surface prepared for the experiments.

Enhanced photovoltaic performance and long-term stability of quasi-solid-state dye-sensitized solar cells via molecular engineering.

Organic dyes with long alkyl chains have been synthesized and demonstrated to be highly efficient sensitizers for liquid and quasi-solid-state solar cells, giving power conversion efficiencies of 8.31-8.39% and 7.03-7.31% under AM 1.5 G irradiation, respectively.

Molecular engineering of organic sensitizers containing p-phenylene vinylene unit for dye-sensitized solar cells.

Three organic sensitizers containing bis-dimethylfluorenyl amino donor and a cyanoacrylic acid acceptor bridged by p-phenylene vinylene unit were synthesized. The power conversion efficiency was quite sensitive to the length of bridged phenylene vinylene groups. A nanocrystalline TiO2 dye-sensitized solar cell was fabricated using three sensitizers. The maximum power conversion efficiency of JK-59 reached 7.02%.

An analytical potential energy function to model protonated peptide soft-landing experiments. The CH3NH3+/CH4 interactions.

To model soft-landing of peptide ions on surfaces, it is important to have accurate intermolecular potentials between these ions and surfaces. As part of this goal, ab initio calculations at the MP2/aug-cc-pVTZ level of theory, with basis set superposition error (BSSE) corrections, were performed to determine both the long-range attractive and short-range repulsive potentials for CH(4) interacting with the -NH(3)(+) group of CH(3)NH(3)(+). Potential energy curves for four different orientations between CH(4) and CH(3)NH(3)(+) were determined from the calculations to obtain accurate descriptions of the interactions between the atoms of CH(4) and those of -NH(3)(+). A universal analytic function was not found that could accurately represent both the long-range and short-range potentials for collision energies as high as those obtained in surface-induced-dissociation (SID) experiments. Instead, long-range and short-range analytic potentials were developed separately, by simultaneously fitting the four ab initio potential energy curves with a sum of two-body interactions between the atoms of CH(4) and -NH(3)(+), and then connecting these long-range and short-range two-body potentials with switching functions. Following a previous work [J. Am. Chem. Soc., 2002, 124, 1524], these two-body potentials may be used to describe the interactions of the N and H atoms of the -NH(3)(+) group of a protonated peptide ion with the H and C atoms of alkane-type surfaces such as alkyl thiol self-assembled monolayers and H-terminated diamond. Accurate short-range and long-range potentials are imperative to model protonated peptide ion soft-landing experiments. The former controls the collision energy transfer, whereas the latter describes the binding of the ion to the surface. A comparison of the ab initio potential energy curves for CH(3)NH(3)(+)/CH(4) with those for NH(4)(+)/CH(4) shows that they give nearly identical two-body interactions between the atoms of -NH(3)(+) and those of CH(4), showing that the smaller NH(4)(+)/CH(4) system may be used to obtain the two-body potentials. A comparison of the four ab initio potential energy curves reported here for CH(3)NH(3)(+)/CH(4), with those given by the AMBER and CHARMM molecular mechanical potentials, show that these latter potentials "roughly" approximate the long-range attractions, but are grossly in error for the short-range repulsions. The work reported here illustrates that high-level ab initio calculations of intermolecular potentials between small model molecules may be used to develop accurate analytical intermolecular potentials between peptide ions and surfaces.

Synthesis and photovoltaic properties of efficient organic dyes containing the benzo[b]furan moiety for solar cells.

New organic dyes composed of the benzo[b]furan donor, thiophene-conjugated bridge, and cyano acrylic acid acceptor have been newly synthesized through the one-pot coupling cyclization key step. Nanocrystalline TiO2 dye-sensitized solar cell was fabricated using this dye. A solar-to-electric conversion efficiency of 6.65% and 4.70% is achieved with 1 and 2, respectively.

Direct dynamics simulations using Hessian-based predictor-corrector integration algorithms.

In previous research [J. Chem. Phys. 111, 3800 (1999)] a Hessian-based integration algorithm was derived for performing direct dynamics simulations. In the work presented here, improvements to this algorithm are described. The algorithm has a predictor step based on a local second-order Taylor expansion of the potential in Cartesian coordinates, within a trust radius, and a fifth-order correction to this predicted trajectory. The current algorithm determines the predicted trajectory in Cartesian coordinates, instead of the instantaneous normal mode coordinates used previously, to ensure angular momentum conservation. For the previous algorithm the corrected step was evaluated in rotated Cartesian coordinates. Since the local potential expanded in Cartesian coordinates is not invariant to rotation, the constants of motion are not necessarily conserved during the corrector step. An approximate correction to this shortcoming was made by projecting translation and rotation out of the rotated coordinates. For the current algorithm unrotated Cartesian coordinates are used for the corrected step to assure the constants of motion are conserved. An algorithm is proposed for updating the trust radius to enhance the accuracy and efficiency of the numerical integration. This modified Hessian-based integration algorithm, with its new components, has been implemented into the VENUS/NWChem software package and compared with the velocity-Verlet algorithm for the H(2)CO-->H(2)+CO, O(3)+C(3)H(6), and F(-)+CH(3)OOH chemical reactions.

Post-transition state dynamics for propene ozonolysis: Intramolecular and unimolecular dynamics of molozonide.

A direct chemical dynamics simulation, at the B3LYP6-31G(d) level of theory, was used to study the post-transition state intramolecular and unimolecular dynamics for the O3 + propene reaction. Comparisons of B3LYP6-31G(d) with CCSD(T)/cc-pVTZ and other levels of theory show that the former gives accurate structures and energies for the reaction's stationary points. The direct dynamics simulations are initiated at the anti and syn O3 + propene transition states (TSs) and the TS symmetries are preserved in forming the molozonide intermediates. Anti<-->syn molozonide isomerization has a very low barrier of 2-3 kcalmol and its Rice-Ramsperger-Kassel-Marcus (RRKM) lifetime is 0.3 ps. However, the trajectory isomerization is slower and it is unclear whether this anti<-->syn equilibration is complete when the trajectories are terminated at 1.6 ps. The syn (anti) molozonides dissociate to CH3CHO + H2COO and H2CO + syn (anti) CH3CHOO. The kinetics for the latter reactions are in overall good agreement with RRKM theory, but there is a symmetry preserving non-RRKM dynamical constraint for the former. Dissociation of anti molozonide to CH3CHO + H2COO is enhanced and suppressed, respectively, for the trajectory ensembles initiated at the anti and syn O3 + propene TSs. The dissociation of syn molozonide to CH3CHO + H2COO may also be enhanced for trajectories initiated at the syn O3 + propene TS. At the time the trajectories are terminated at 1.6 ps, the ratio of the trajectory and RRKM values of the CH3CHO + H2COO product yield is 1.6 if the symmetries of the initiation and dissociation TSs are the same and 0.6 if their symmetries are different. There are coherences in the intramolecular energy flow, which depend on molozonide's symmetry (i.e., anti or syn). This symmetry related dynamics is not completely understood, but it is clearly related to the non-RRKM dynamics for anti<-->syn isomerization and anti molozonide dissociation to CH3CHO + H2COO. Correlations are found between the stretching motions of molozonide, indicative of nonchaotic and non-RRKM dynamics. The non-RRKM dynamics of molozonide dissociation partitions vibration energy to H2COO that is larger than statistical partitioning. Though the direct dynamics simulations are classical, better agreement is obtained using quantum instead of classical harmonic RRKM theory. This may result from the neglect of anharmonicity in the RRKM calculations, the non-RRKM dynamics of the classical trajectories, or a combination of these two effects. The trajectories suggest that the equilibrium syn/anti molozonide ratio is approximately 1.1-1.2 times larger than that predicted by the harmonic densities of state, indicating an anharmonic correction.

Use of a single trajectory to study product energy partitioning in unimolecular dissociation: mass effects for halogenated alkanes.

A single trajectory (ST) direct dynamics approach is compared with quasiclassical trajectory (QCT) direct dynamics calculations for determining product energy partitioning in unimolecular dissociation. Three comparisons are made by simulating C(2)H(5)F-->HF + C(2)H(4) product energy partitioning for the MP26-31G(*) and MP26-311 + + G(**) potential energy surfaces (PESs) and using the MP26-31G(*) PES for C(2)H(5)F dissociation as a model to simulate CHCl(2)CCl(3)-->HCl + C(2)Cl(4) dissociation and its product energy partitioning. The trajectories are initiated at the transition state with fixed energy in reaction-coordinate translation E(t) (double dagger). The QCT simulations have zero-point energy (ZPE) in the vibrational modes orthogonal to the reaction coordinate, while there is no ZPE for the STs. A semiquantitative agreement is obtained between the ST and QCT average percent product energy partitionings. The ST approach is used to study mass effects for product energy partitioning in HX(X = F or Cl) elimination from halogenated alkanes by using the MP26-31G(*) PES for C(2)H(5)F dissociation and varying the masses of the C, H, and F atoms. There is, at most, only a small mass effect for partitioning of energy to HX vibration and rotation. In contrast, there are substantial mass effects for partitioning to relative translation and the polyatomic product's vibration and rotation. If the center of mass of the polyatomic product is located away from the C atom from which HX recoils, the polyatomic has substantial rotation energy. Polyatomic products, with heavy atoms such as Cl atoms replacing the H atoms, receive substantial vibration energy that is primarily transferred to the wag-bend motions. For E(t) (double dagger) of 1.0 kcalmol, the ST calculations give average percent partitionings to relative translation, polyatomic vibration, polyatomic rotation, HX vibration, and HX rotation of 74.9%, 6.8%, 1.5%, 14.4%, and 2.4% for C(2)H(5)F dissociation and 39.7%, 38.1%, 0.2%, 16.1%, and 5.9% for a model of CHCl(2)CCl(3) dissociation.

Comparison of levels of electronic structure theory in direct dynamics simulations of C2H5F --> HF + C2H4 product energy partitioning.

Direct dynamics simulations at the MP2/6-311++G** level of theory were performed to study C(2)H(5)F --> HF + C(2)H(4) product energy partitioning. The simulation results are compared with experiment and a previous MP2/6-31G* simulation. The current simulation with the larger basis set releases more energy to HF vibration and less to HF + C(2)H(4) relative translation as compared to the previous simulation with the 6-31G* basis set. The HF rotation and vibration energy distributions determined from the current simulation are in overall very good agreement with previous experimental studies of C(2)H(5)F dissociation by chemical activation and IRMPA. A comparison of the simulations with experiments suggests there may be important mass effects for energy partitioning in HX elimination from haloalkanes. The transition state (TS) structures and energies calculated with MP2 and the 6-31G* and 6-311++G** basis sets are compared with those calculated using CCD, CCSD, CCSD(T), and the 6-311++G** basis set.