Ab initio molecular dynamics modeling of single polyethylene chains: Scission kinetics and influence of radical under mechanical strain.

Ab initio molecular dynamics was used to estimate the response to constant imposed strain on a short polyethylene (PE) chain and a radical chain with a removed hydrogen atom. Two independent types of simulations were run. In the first case, the chains were strained by expanding a periodic cell, restraining the length but allowing the internal degrees of freedom to reach equilibrium. From these simulations, the average force on the chain was computed, and the resulting force was integrated to determine the Helmholtz free energy for chain stretching. In the second set of simulations, chains were constrained to various lengths, while a bond was restrained at various bond lengths using umbrella sampling. This provided free energy of bond scission for various chain strains. The sum of the two free energy functions results in an approximation of the free energy of chain scission under various strains and gives a realistic and new picture of the effect of chain strain on bond breaking. Unimolecular scission rates for each chain type were examined as a function of chain strain. The scission rate for the radical chain is several orders of magnitude larger than that of the pristine chain at smaller strains and at equilibrium. This highlights the importance of radical formation in PE rupture and is consistent with experiments. Constant strain results were used to derive a constant-force model for the radical chain that demonstrates a roll over in rate similar to the "catch-bond" behavior observed in protein membrane detachment experiments.

Analytic non-adiabatic derivative coupling terms for spin-orbit MRCI wavefunctions. I. Formalism.

Analytic gradients of electronic eigenvalues require one calculation per nuclear geometry, compared to at least 3n + 1 calculations for finite difference methods, where n is the number of nuclei. Analytic nonadiabatic derivative coupling terms (DCTs), which are calculated in a similar fashion, are used to remove nondiagonal contributions to the kinetic energy operator, leading to more accurate nuclear dynamics calculations than those that employ the Born-Oppenheimer approximation, i.e., that assume off-diagonal contributions are zero. The current methods and underpinnings for calculating both of these quantities, gradients and DCTs, for the State-Averaged MultiReference Configuration Interaction with Singles and Doubles (MRCI-SD) wavefunctions in COLUMBUS are reviewed. Before this work, these methods were not available for wavefunctions of a relativistic MRCI-SD Hamiltonian. Calculation of these terms is critical in successfully modeling the dynamics of systems that depend on transitions between potential energy surfaces split by the spin-orbit operator, such as diode-pumped alkali lasers. A formalism for calculating the transition density matrices and analytic derivative coupling terms for such systems is presented.

Analytic non-adiabatic derivative coupling terms for spin-orbit MRCI wavefunctions. II. Derivative coupling terms and coupling angle for KHeA2Π1/2⇔KHeB2Σ1/2.

A method for calculating the analytic nonadiabatic derivative coupling terms (DCTs) for spin-orbit multi-reference configuration interaction wavefunctions is reviewed. The results of a sample calculation using a Stuttgart basis for KHe are presented. Additionally, the DCTs are compared with a simple calculation based on the Nikitin's 3 × 3 description of the coupling between the Σ and Π surfaces, as well as a method based on Werner's analysis of configuration interaction coefficients. The nonadiabatic coupling angle calculated by integrating the radial analytic DCTs using these different techniques matches extremely well. The resultant nonadiabatic energy surfaces for KHe are presented.

Bond breaking in epoxy systems: A combined QM/MM approach.

A novel method to combine quantum mechanics (QM) and molecular mechanics has been developed to accurately and efficiently account for covalent bond breaking in polymer systems under high strain without the use of predetermined break locations. Use of this method will provide a better fundamental understanding of the mechano-chemical origins of fracture in thermosets. Since classical force fields cannot accurately account for bond breaking, and QM is too demanding to simulate large systems, a hybrid approach is required. In the method presented here, strain is applied to the system using a classical force field, and all bond lengths are monitored. When a bond is stretched past a threshold value, a zone surrounding the bond is used in a QM energy minimization to determine which, if any, bonds break. The QM results are then used to reconstitute the system to continue the classical simulation at progressively larger strain until another QM calculation is triggered. In this way, a QM calculation is only computed when and where needed, allowing for efficient simulations. A robust QM method for energy minimization has been determined, as well as appropriate values for the QM zone size and the threshold bond length. Compute times do not differ dramatically from classical molecular mechanical simulations.

Computation of the binding free energy of peptides to graphene in explicit water.

The characteristic properties of graphene make it useful in an assortment of applications. One particular application--the use of graphene in biosensors--requires a thorough understanding of graphene-peptide interactions. In this study, the binding of glycine (G) capped amino acid residues (termed GXG tripeptides) to trilayer graphene surfaces in aqueous solution was examined and compared to results previously obtained for peptide binding to single-layer free-standing graphene [A. N. Camden, S. A. Barr, and R. J. Berry, J. Phys. Chem. B 117, 10691-10697 (2013)]. In order to understand the interactions between the peptides and the surface, binding enthalpy and free energy values were calculated for each GXG system, where X cycled through the typical 20 amino acids. When the GXG tripeptides were bound to the surface, distinct conformations were observed, each with a different binding enthalpy. Analysis of the binding energy showed the binding of peptides to trilayer graphene was dominated by van der Waals interactions, unlike the free-standing graphene systems, where the binding was predominantly electrostatic in nature. These results demonstrate the utility of computational materials science in the mechanistic explanation of surface-biomolecule interactions which could be applied to a wide range of systems.

M + Ng potential energy curves including spin-orbit coupling for M = K, Rb, Cs and Ng = He, Ne, Ar.

The X(2)Σ(1/2)(+), A(2)Π(1∕2), A(2)Π(3∕2), and B(2)Σ(1/2)(+) potential energy curves and associated dipole matrix elements are computed for M + Ng at the spin-orbit multi-reference configuration interaction level, where M = K, Rb, Cs and Ng = He, Ne, Ar. Dissociation energies and equilibrium positions for all minima are identified and corresponding vibrational energy levels are computed. Difference potentials are used together with the quasistatic approximation to estimate the position of satellite peaks of collisionally broadened D2 lines. The comparison of potential energy curves for different alkali atom and noble gas atom combinations is facilitated by using the same level of theory for all nine M + Ng pairs.

Structural reorganizations control intermolecular conductance and charge trapping in paraquat-tetraphenylborate inverse photochemical cell.

Miniaturization of electronic devices to the level of single molecules requires detailed understanding of the mechanisms of their operation. One of the questions here is the identification of the role of structural alterations in charge separation and stabilization in photoactive complexes. To address this question, we calculate optimized molecular and electronic structures, and optical and vibrational spectra of l,l'-dimethyl 4,4'-bipyridinium-bis tetraphenylborate PQ(BPh(4))(2) complex ab initio using density functional theory approach and compare them with the experimentally observed UV-Vis and Raman spectra of the molecules in solid-state films. The results indicate that the association of PQ and BPh(4) leads to the formation of an internally ionized structure that is accompanied by the structural reorganization of both PQ (the twisting of pyridinium rings) and BPh(4) (phenyl rings rotation) moieties. The quanta of light do not seem to be directly involved in the formation of this ionized structure, but provide energy for fast recombination of the separated charges between BPh(4)(-) and PQ(2+). The high efficiency of the dark charge separation and the stabilization of separated charges in the complex permit the using of PQ(BPh(4))(2) in various charge-transfer devices like molecular probes, photovoltaic devices or chemical memory units.