Developing accurate molecular mechanics force fields for conjugated molecular systems

A rapid method to parameterize the intramolecular component of classical force fields for complex conjugated molecules is proposed. The method is based on a procedure of force matching with a reference electronic structure calculation. It is particularly suitable for those applications where molecular dynamics simulations are used to generate structures that are therefore analysed by electronic structure methods, because it is possible to build force fields that are consistent with electronic structure calculations that follow classical simulations. Such applications are commonly encountered in organic electronics, spectroscopy of complex systems and photobiology (e.g. photosynthetic systems). We illustrate the method by parameterizing the force fields of a molecule used in molecular semiconductors (2,2-dicyanovinyl-capped S,N-heteropentacene or DCV-SN5), a polymeric semiconductor (thieno[3,2-b]thiophene-diketopyrrolopyrrole TT-DPP) and a chromophore embedded in a protein environment (15,16-dihydrobiliverdin or DBV) where several hundreds of parameters need to be optimized in parallel

Structural optimization of molecular clusters with density functional theory combined with basin hopping

Identifying the energy minima of molecular clusters is a challenging problem. Traditionally, search algorithms such as simulated annealing, genetic algorithms, or basin hopping are usually used in conjunction with empirical force fields. We have implemented a basin hopping search algorithm combined with density functional theory to enable the optimization of molecular clusters without the need for empirical force fields. This approach can be applied to systems where empirical potentials are not available or may not be sufficiently accurate. We illustrate the effectiveness of the method with studies on water, methanol, and water + methanol clusters as well as protonated water and methanol clusters at the B3LYP+D/6-31+G* level of theory. A new lowest energy structure for H+(H2O)7 is predicted at the B3LYP+D/6-31+G* level. In all of the protonated mixed water and methanol clusters, we find that H+ prefers to combine with methanol rather than water in the lowest-energy structures

Structural optimization of molecular clusters with density functional theory combined with basin hopping

Identifying the energy minima of molecular clusters is a challenging problem. Traditionally, search algorithms such as simulated annealing, genetic algorithms, or basin hopping are usually used in conjunction with empirical force fields. We have implemented a basin hopping search algorithm combined with density functional theory to enable the optimization of molecular clusters without the need for empirical force fields. This approach can be applied to systems where empirical potentials are not available or may not be sufficiently accurate. We illustrate the effectiveness of the method with studies on water, methanol, and water + methanol clusters as well as protonated water and methanol clusters at the B3LYP+D/6-31+G* level of theory. A new lowest energy structure for H+(H2O)7 is predicted at the B3LYP+D/6-31+G* level. In all of the protonated mixed water and methanol clusters, we find that H+ prefers to combine with methanol rather than water in the lowest-energy structures

Structure and bonding in ionized water clusters

The structure and bonding in ionized water clusters, (H_2O)n+(n = 3–9), has been studied using the basin hopping search algorithm in combination with quantum chemical calculations. Initially candidate low energy isomers are generated using basin hopping in conjunction with density functional theory. Subsequently, the structures and energies are refined using second order Moller-Plesset perturbation theory and coupled cluster theory, respectively. The lowest energy isomers are found to involve proton transfer to give H_3O+ and a OH radical, which are more stable than isomers containing the hemibonded hydrazine-like fragment (H_2O-OH_2), with the calculated infrared spectra consistent with experimental data. For (H_2O)_9^+ the observation of a new structural motif comprising proton transfer to form H_3O^+ and OH, but with the OH radical involved in hemibonding to another water molecule is discussed

Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins

The calculation of the electronic circular dichroism (CD) spectra of the oxidised form of the blue copper proteins plastocyanin and cucumber basic protein and the relationship between the observed spectral features and the structure of the active site of the protein is investigated. Excitation energies and transition strengths are computed using multi reference configuration interaction, and it is shown that computed spectra based on coordinates from the crystal structure or a single structure optimised in quantum mechanics/molecular mechanics (QM/MM) or ligand field molecular mechanics (LFMM) are qualitatively incorrect. In particular, the rotational strength of the ligand to metal charge transfer band is predicted to be too small or have the incorrect sign. By considering calculations on active site models with modified structures it is shown that the intensity of this band is sensitive to the non-planarity of the histidine and cysteine ligands coordinated to copper. Calculation of the ultraviolet absorption and CD spectra based upon averaging over many structures drawn from a LFMM molecular dynamics simulation are in good agreement with experiment, and superior to analogous calculations based upon structures from a classical molecular dynamics simulation. This provides evidence that the LFMM force field provides an accurate description of the molecular dynamics of these proteins

Structural optimization of molecular clusters with density functional theory combined with basin hopping

Identifying the energy minima of molecular clusters is a challenging problem. Traditionally, search algorithms such as simulated annealing, genetic algorithms, or basin hopping are usually used in conjunction with empirical force fields. We have implemented a basin hopping search algorithm combined with density functional theory to enable the optimization of molecular clusters without the need for empirical force fields. This approach can be applied to systems where empirical potentials are not available or may not be sufficiently accurate. We illustrate the effectiveness of the method with studies on water, methanol, and water + methanol clusters as well as protonated water and methanol clusters at the B3LYP+D/6-31+G* level of theory. A new lowest energy structure for H+(H2O)7 is predicted at the B3LYP+D/6-31+G* level. In all of the protonated mixed water and methanol clusters, we find that H+ prefers to combine with methanol rather than water in the lowest-energy structures

Dynamic Disorder Drives Exciton Dynamics in Diketopyrrolopyrrole - Thiophene-containing Molecular Crystals

There is a growing interest in controllable molecular materials for potential nanophotonic and quantum information applications where excitons move beyond the incoherent transport regime. Thus, the ability to identify the key parameters that correlate with the efficiency of the transport of the excitation energy is highly desirable. In this work, we investigate the effects of the dynamic disorder on the transport of the exciton in molecular crystals of several mono- and dialkylated 1,4-diketo-3,6-dithiophenylpyrrolo[3-4-c]pyrrole derivatives. These systems exhibit great potential for photovoltaic applications due to their broad optical absorption and efficient charge transport. The exciton dynamics are studied using a model Hamiltonian, in which the thermal fluctuations of the excitonic coupling (nonlocal electron−phonon coupling), as well as the local exciton−phonon couplings, have been appropriately taken into account. The computed reorganization energies for the most feasible transport pathway (π−π stacking) for the excitons in UBEQUQ and UBEQOK molecular crystals are 0.366 and 0.357 eV, respectively. These values are comparable with the magnitude of the average excitonic coupling ⟨J⟩ (≈ 0.1 eV) for these two molecular crystals. In this instance, the local exciton−phonon coupling is not large enough to form a small exciton-polaron. In addition, substantial coherences are observed on a time scale of less than 100 fs, whichindicates that the dynamic disorder is sufficient to overcome quantum dephasing and help drive exciton transport in this class of organic semiconductors. On the other hand, the diffusion of the excitons reduces significantly when the thermal fluctuations of theexcitonic coupling are omitted. Thus, dynamic disorder plays a vital role in the transport of the exciton, and the ability to control this inherent property in molecular aggregates will provide valuable tools for the design and development of efficient organic semiconductors

Electronic circular dichroism of proteins computed using a diabatisation scheme

Circular dichroism (CD) spectroscopy is a powerful technique employed to study the structure of biomolecules. More accurate calculation of CD from first principles will aid both computational and experimental studies of protein structure and dynamics. We apply a diabatisation scheme to improve the description of nearest neighbour interactions between two electronic transitions (nπ* and πnbπ*) localised on each individual peptide bond (amide group) in a protein. These interactions are incorporated into DichroCalc, an exciton-based computational method to calculate CD, and yield improvements over the standard DichroCalc parameter set, particularly for calculation of CD for important secondary structural elements such as an α helix

Force fields for macromolecular assemblies containing Diketopyrrolopyrrole and Thiophene

Utilizing a force-matching procedure, we parametrize new force fields systematically for large conjugated systems. We model both conjugated polymers and molecular crystals that contain diketopyrrolopyrrole, thiophene, and thieno[3,2-b]thiophene units. These systems have recently been found to have low band gaps, which exhibit high efficiency for photovoltaic devices. The equilibrium structures, forces, and energies of the building block chromophores, diketopyrrolopyrrole, thiophene, and thieno[3,2-b]thiophene computed using our parameters are comparable to those computed using the reference electronic structure method. We assess the suitability of this new force field for electronic property calculations by comparing the electronic excitation properties computed along classical and ab initio molecular dynamics trajectories. For both trajectories, we find similar distributions of TDDFT-calculated excitation energies and oscillator strengths for the building block chromophore diketopyrrolopyrrole-thieno[3,2-b]thiophene. The structural, dynamic, and electronic properties of the macromolecular assemblies built upon these chromophores are characterized. For both polymers and molecular crystals, pronounced peaks around 0° or 180° are observed for the torsions between chromophores under ambient conditions. The high planarity in these systems can promote local ordering and π–π stacking, thereby potentially facilitating charge transport across these materials. For the model conducting polymers, we found that the fluctuations in the density of states per chain per monomer is negligibly small and does not vary significantly with chains comprising 20–40 monomers. Analysis of the electron–hole distributions and the transition density matrices indicates that the delocalized length is approximately 4–6 monomers, which is in good agreement with other theoretical and experimental studies of different conducting polymers. For the molecular crystals, our investigation of the characteristic time scale of the fluctuation in the excitonic couplings shows that a low-frequency vibration below 100 cm–1 is observed for the nearest neighbors. These observations are in line with previous studies on other molecular crystals, in which low-frequency vibrations are believed to be responsible for the large modulation of the excitonic coupling. Thus, our approach and the new force fields provide a direct route for studying the structure–property relations and the molecular level origins of the high efficiency of these classes of materials

Cluster integrals and virial coefficients for realistic molecular models

We present a concise, general, and efficient procedure for calculating the cluster integrals that relate thermodynamic virial coefficients to molecular interactions. The approach encompasses nonpairwise intermolecular potentials generated from quantum chemistry or other sources; a simple extension permits efficient evaluation of temperature and other derivatives of the virial coefficients. We demonstrate with a polarizable model of water. We argue that cluster-integral methods are a potent yet underutilized instrument for the development and application of first-principles molecular models and methods