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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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)(+).

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.

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

In previous research [J. Chem. Phys.

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.

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).

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.

Direct dynamics trajectory study of the reaction of formaldehyde cation with D2: vibrational and zero-point energy effects on quasiclassical trajectories.

Quasiclassical, direct dynamics trajectories have been used to study the reaction of formaldehyde cation with molecular hydrogen, simulating the conditions in an experimental study of H2CO+ vibrational effects on this reaction. Effects of five different H2CO+ modes were probed, and we also examined different approaches to treating zero-point energy in quasiclassical trajectories. The calculated absolute cross-sections are in excellent agreement with experiments, and the results provide insight into the reaction mechanism, product scattering behavior, and energy disposal, and how they vary with impact parameter and reactant state.

Direct dynamics trajectory study of vibrational effects: can polanyi rules be generalized to a polyatomic system?

We present an ab initio direct dynamics trajectory study of the hydrogen abstraction reaction: H2CO+ + CD4 --> H2COD+ + CD3, with methane excited in two different distortion modes (nu4 and nu2). The trajectory simulations were able to reproduce experimental results and for the first time show how vibrational enhancement originates in reaction of small polyatomic species. Roughly equal contributions from two vibrational enhancement mechanisms were found.

Direct dynamics study of N-protonated diglycine surface-induced dissociation. Influence of collision energy.

A quantum mechanical and molecular mechanical (QM + MM) direct dynamics classical trajectory simulation is used to study energy transfer and fragmentation in the surface-induced dissociation (SID) of N-protonated diglycine, (gly)2H+. The peptide ion collides with the hydrogenated diamond [111] surface. The Austin Model 1 (AM1) semiempirical electronic structure theory is used for the (gly)2H+ intramolecular potential and molecular mechanical functions are used for the diamond surface potential and peptide/surface intermolecular potential.

A SN2 reaction that avoids its deep potential energy minimum.

Chemical dynamics trajectory simulations were used to study the atomic-level mechanisms of the OH- + CH3F --> CH3OH + F- SN2 nucleophilic substitution reaction. The reaction dynamics, from the [OH..