Beth A. Lindquist

Nitrile Groups as Vibrational Probes: Calculations of the C≡N Infrared Absorption Line Shape of Acetonitrile in Water and Tetrahydrofuran

The C[TRIPLE BOND]N bond is a powerful probe of protein structure and dynamics because it absorbs in a region of the infrared spectrum apart from the other vibrations that occur naturally in proteins, and because its infrared absorption line shape is sensitive to specific characteristics of the local environment. Since the polarity experienced by the probe can differ dramatically within the protein, infrared spectroscopy of a C[TRIPLE BOND]N site-specifically labeled residue can be used to infer its local environment within the protein. It has been shown experimentally that the spectrum of acetonitrile in water is different in terms of peak position and width compared to acetonitrile in tetrahydrofuran (THF). An optimized quantum mechanics/molecular mechanics method for calculating accurate vibrational frequencies in condensed-phase was parametrized for acetonitrile in water. The transferability of the methodology to a different solvent was tested by computing the infrared line shapes of acetonitrile in both water and THF and comparing to experiment. The infrared absorption line shapes agree well with experiment in each case, and the trends observed experimentally are recovered. The accuracy of the methodology for two solvents of differing polarity indicates that this technique is suitable to study CN probes in proteins.

Optimized quantum mechanics/molecular mechanics strategies for nitrile vibrational probes: acetonitrile and para-tolunitrile in water and tetrahydrofuran.

The nitrile (Ctriple bondN) group is a powerful probe of structure and dynamics because its vibrational frequency is extraordinarily sensitive to the electrostatic and chemical characteristics of its local environment. For example, site-specific nitrile labels are useful indicators of protein structure because their infrared (IR) absorption spectra can clearly distinguish between solvent-exposed residues and residues buried in the hydrophobic core of a protein. In this work, three variants of the optimized quantum mechanics/molecular mechanics (OQM/MM) technique for computing Ctriple bondN vibrational frequencies were developed and assessed for acetonitrile in water. For the most robust variant, the transferability of the OQM/MM methodology to different solutes and solvents was evaluated by simulating the IR absorption spectra of para-tolunitrile in water and tetrahydrofuran and comparing to experiment and density functional theory (DFT) calculations. The OQM/MM frequencies compared favorably to DFT for para-tolunitrile/water, and the calculated IR absorption spectra are in qualitative agreement with experiment. This suggests that a single parametrization of the OQM/MM technique is reasonable for the calculation of nitrile line shapes when the probe is attached to different chemical moieties and when the label experiences local environments of different polarity.

Bonding in Sulfur–Oxygen Compounds—HSO/SOH and SOO/OSO: An Example of Recoupled Pair π Bonding

The ground states (X(2)A″) of HSO and SOH are extremely close in energy, yet their molecular structures differ dramatically, e.g., re(SO) is 1.485 Å in HSO and 1.632 Å in SOH. The SO bond is also much stronger in HSO than in SOH: 100.3 kcal/mol versus 78.8 kcal/mol [RCCSD(T)-F12/AVTZ]. Similar differences are found in the SO2 isomers, SOO and OSO, depending on whether the second oxygen atom binds to oxygen or sulfur. We report generalized valence bond and RCCSD(T)-F12 calculations on HSO/SOH and OSO/SOO and analyze the bonding in all four species. We find that HSO has a shorter and stronger SO bond than SOH due to the presence of a recoupled pair bond in the π(a″) system of HSO. Similarly, the bonding in SOO and OSO differs greatly. SOO is like ozone and has substantial diradical character, while OSO has two recoupled pair π bonds and negligible diradical character. The ability of the sulfur atom to form recoupled pair bonds provides a natural explanation for the dramatic variation in the bonding in these and many other sulfur-oxygen compounds.

Solvation dynamics of Hoechst 33258 in water: an equilibrium and nonequilibrium molecular dynamics study.

Integrated within an appropriate theoretical framework, molecular dynamics (MD) simulations are a powerful tool to complement experimental studies of solvation dynamics. Together, experiment, theory, and simulation have provided substantial insight into the dynamic behavior of polar solvents. MD investigations of solvation dynamics are especially valuable when applied to the heterogeneous environments found in biological systems, where the calculated response of the environment to the electrostatic perturbation of the probe molecule can easily be decomposed by component (e.g., aqueous solvent, biomolecule, ions), greatly aiding the molecular-level interpretation of experiments. A comprehensive equilibrium and nonequilibrium MD study of the solvation dynamics of the fluorescent dye Hoechst 33258 (H33258) in aqueous solution is presented. Many fluorescent probes employed in experimental studies of solvation dynamics in biological systems, such as the DNA minor groove binder H33258, have inherently more conformational flexibility than prototypical fused-ring chromophores. The role of solute flexibility was investigated by developing a fully flexible force-field for the H33258 molecule and by simulating its solvation response. While the timescales for the total solvation response calculated using both rigid (0.16 and 1.3 ps) and flexible (0.17 and 1.4 ps) models of the probe closely matched the experimentally measured solvation response (0.2 and 1.2 ps), there were subtle differences in the response profiles, including the presence of significant oscillations for the flexible probe. A decomposition of the total response of the flexible probe revealed that the aqueous solvent was responsible for the overall decay, while the oscillations result from fluctuations in the electrostatic terms in the solute intramolecular potential energy. A comparison of equilibrium and nonequilibrium approaches for the calculation of the solvation response confirmed that the solvation dynamics of H33258 in water is well-described by linear response theory for both rigid and flexible models of the probe.

Insights into the Electronic Structure of Molecules from Generalized Valence Bond Theory

In this article we describe the unique insights into the electronic structure of molecules provided by generalized valence bond (GVB) theory. We consider selected prototypical hydrocarbons as well as a number of hypervalent molecules and a set of first- and second-row valence isoelectronic species. The GVB wave function is obtained by variationally optimizing the orbitals and spin coupling in the valence bond wave function. The GVB wave function is a generalization of the Hartree-Fock (HF) wave function, lifting the double occupancy restriction on a subset of the HF orbitals as well as the associated orthogonality and spin coupling constraints. The GVB wave function includes a major fraction (if not all) of the nondynamical correlation energy of a molecule. Because of this, GVB theory properly describes bond formation and can answer one of the most compelling questions in chemistry: How are atoms changed by molecular formation? We show that GVB theory provides a unified description of the nature of the bonding in all of the above molecular species as well as contributing new insights into the well-known, but poorly understood, first-row anomaly.

Linking Semiconductor Nanocrystals into Gel Networks through All‐Inorganic Bridges

For colloidal semiconductor nanocrystals (NCs), replacement of insulating organic capping ligands with chemically diverse inorganic clusters enables the development of functional solids in which adjacent NCs are strongly coupled. Yet controlled assembly methods are lacking to direct the arrangement of charged, inorganic cluster-capped NCs into open networks. Herein, we introduce coordination bonds between the clusters capping the NCs thus linking the NCs into highly open gel networks. As linking cations (Pt(2+)) are added to dilute (under 1 vol %) chalcogenidometallate-capped CdSe NC dispersions, the NCs first form clusters, then gels with viscoelastic properties. The phase behavior of the gels for variable [Pt(2+)] suggests they may represent nanoscale analogues of bridged particle gels, which have been observed to form in certain polymer colloidal suspensions.

Communication: Inverse design for self-assembly via on-the-fly optimization

Inverse methods of statistical mechanics have facilitated the discovery of pair potentials that stabilize a wide variety of targeted lattices at zero temperature. However, such methods are complicated by the need to compare, within the optimization framework, the energy of the desired lattice to all possibly relevant competing structures, which are not generally known in advance. Furthermore, ground-state stability does not guarantee that the target will readily assemble from the fluid upon cooling from higher temperature. Here, we introduce a molecular dynamics simulation-based, optimization design strategy that iteratively and systematically refines the pair interaction according to the fluid and crystalline structural ensembles encountered during the assembly process. We successfully apply this probabilistic, machine-learning approach to the design of repulsive, isotropic pair potentials that assemble into honeycomb, kagome, square, rectangular, truncated square, and truncated hexagonal lattices.

Probabilistic inverse design for self-assembling materials

One emerging approach for the fabrication of complex architectures on the nanoscale is to utilize particles customized to intrinsically self-assemble into a desired structure. Inverse methods of statistical mechanics have proven particularly effective for the discovery of interparticle interactions suitable for this aim. Here we evaluate the generality and robustness of a recently introduced inverse design strategy [B. A. Lindquist et al., J. Chem. Phys. 145, 111101 (2016)] by applying this simulation-based machine learning method to optimize for interparticle interactions that self-assemble particles into a variety of complex microstructures as follows: cluster fluids, porous mesophases, and crystalline lattices. Using the method, we discover isotropic pair interactions that lead to the self-assembly of each of the desired morphologies, including several types of potentials that were not previously understood to be capable of stabilizing such systems. One such pair potential led to the assembly of the hi...

Insights into the electronic structure of disulfur tetrafluoride isomers from generalized valence bond theory.

Sulfur and fluorine can participate in a variety of bonding motifs, lending significant diversity to their chemistry. Prior work has identified three distinct minima for disulfur tetrafluoride (S2F4) compounds: two FSSF3 isomers and one SSF4 species. We used a combination of sophisticated explicitly correlated coupled cluster calculations and generalized valence bond (GVB) theory to characterize the electronic structure of these species as well as additional stationary points on the potential energy surface with F2SSF2 connectivity. On the singlet surface, the two stationary points considered in this work with an F2SSF2 structure are first- or second-order saddle points and not minima. However, on the triplet surface, we discovered a novel C2 symmetric F2SSF2 minimum that was anticipated from the structure of an excited state ((3)B1) of SF2. Analysis using the GVB wave function in conjunction with the recoupled pair bonding model developed by our group provides a straightforward explanation of the bonding in all of the S2F4 structures considered here. In addition, the model predicted the existence of the F2SSF2((3)B) minimum.

Effects of Ligand Electronegativity on Recoupled Pair Bonds with Application to Sulfurane Precursors

Recoupled pair bonds (RPBs) are conditional bonds-they only form for selected central atoms and ligands. A complete theoretical description of RPBs requires an understanding of the properties of the central atom and ligands that enable such bonds to be formed. In this work, we show that ligand electronegativity is positively correlated with recoupled pair bond strength for a variety of ligands interacting with the 3p(2) pair of sulfur. We also describe substituent (X) effects on the SF(a(4)Σ(-)) state by investigating X2SF species. These effects generally mirror those observed for covalently bound analogues, but we found that recoupled pair bonding can lead to breakdowns in the expected relationships among bond length, strength, and force constant for some of these species. Finally, we compare the properties of two molecules of practical interest that are bound by recoupled pair bonds: the dimethyl sulfur fluoride and hydroxide radicals (DMS-F and DMS-OH).