Controlling Monoterpene Isomerization by Guiding Challenging Carbocation Rearrangement Reactions in Engineered Squalene-Hopene Cyclases.

The interconversion of monoterpenes is facilitated by a complex network of carbocation rearrangement pathways. Controlling these isomerization pathways is challenging when using common Brønsted and Lewis acid catalysts, which often produce product mixtures that are difficult to separate. In contrast, natural monoterpene cyclases exhibit high control over the carbocation rearrangement reactions but are reliant on phosphorylated substrates. In this study, we present engineered squalene-hopene cyclases from Alicyclobacillus acidocaldarius (AacSHC) that catalyze the challenging isomerization of monoterpenes with unprecedented precision. Starting from a promiscuous isomerization of (+)-ß-pinene, we first demonstrate noticeable shifts in the product distribution solely by introducing single point mutations. Furthermore, we showcase the tuneable cation steering by enhancing (+)-borneol selectivity from 1 % to >90 % (>99 % de) aided by iterative saturation mutagenesis. Our combined experimental and computational data suggest that the reorganization of key aromatic residues leads to the restructuring of the water network that facilitates the selective termination of the secondary isobornyl cation. This work expands our mechanistic understanding of carbocation rearrangements and sets the stage for target-oriented skeletal reorganization of broadly abundant terpenes.

Anisotropic pressure effects on nanoconfined water within narrow graphene slit pores.

There is an increasing interest toward disclosing and explaining confinement effects on liquids, such as water or aqueous solutions, in slit pore setups. Particularly puzzling are the changes of physical and chemical properties in the nanoconfinement regime where no bulk-like water phase exists between the two interfacial water layers such that the density profile across the slit pore becomes highly stratified, ultimately leading to bilayer and monolayer water. These changes must be quantified with respect to some meaningful reference state of water, the most natural one being bulk water at the same pressure and temperature conditions. However, bulk water is a homogeneous liquid with isotropic properties, whereas water confined in slit pores is inhomogeneous, implying anisotropic properties as described by the perpendicular and parallel components of the respective tensors. In the case of pressure, the inhomogeneous nature of the setup results in a well-defined difference between the perpendicular and parallel pressure tensor components that is uniquely determined by the interfacial tension being a thermodynamic property. For bilayer water constrained in graphene slit pores that are only about 1 nm wide, we demonstrate that there exists a thermodynamic point where the pressure tensor of the inhomogeneous fluid, nanoconfined water, is effectively isotopic and the pressure is thus scalar as in the homogeneous fluid, bulk water. This specific point of vanishing effective interfacial tension is proposed to serve as a well-defined reference state to compare the properties of nanoconfined liquids to those of the corresponding bulk liquid at the same (isotropic) pressure and temperature conditions. In future work, this idea could be applied to assess confinement effects on chemical reactivity in aqueous solutions as well as to other nanoconfined liquids in other pores such as layered minerals.

C-H Bonds as Functional Groups: Simultaneous Generation of Multiple Stereocenters by Enantioselective Hydroxylation at Unactivated Tertiary C-H Bonds.

Enantioselective C-H oxidation is a standing chemical challenge foreseen as a powerful tool to transform readily available organic molecules into precious oxygenated building blocks. Here, we describe a catalytic enantioselective hydroxylation of tertiary C-H bonds in cyclohexane scaffolds with H2O2, an evolved manganese catalyst that provides structural complementary to the substrate similarly to the lock-and-key recognition operating in enzymatic active sites. Theoretical calculations unveil that enantioselectivity is governed by the precise fitting of the substrate scaffold into the catalytic site, through a network of complementary weak non-covalent interactions. Stereoretentive C(sp3)-H hydroxylation results in a single-step generation of multiple stereogenic centers (up to 4) that can be orthogonally manipulated by conventional methods providing rapid access, from a single precursor to a variety of chiral scaffolds.

Deciphering the Properties of Nanoconfined Aqueous Solutions by Vibrational Sum Frequency Generation Spectroscopy.

When confined between walls at nanometer distances, water exhibits surprisingly different properties with reference to bare interfacial water. Based on computer simulations, we demonstrate how vibrational sum frequency generation (VSFG) spectroscopy can be used-even with very mild symmetry breaking-to discriminate multilayer water in wide slit pores from both bilayer and monolayer water confined within molecularly narrow pores. Applying the technique, the VSFG lineshapes of monolayer, bilayer, and multilayer water are found to differ in characteristic ways, which is explained by their distinct density stratifications giving rise to different H-bonding patterns in the respective solvation layers.

Nanoconfinement effects on water in narrow graphene-based slit pores as revealed by THz spectroscopy.

The properties of water at interfaces have long been known to differ from those of bulk water in many distinctive ways. More recently, specific confinement effects different from mere interfacial effects have been discovered upon enclosing water in very narrow cylindrical pores and planar surfaces as offered by nanotubes and slit pores, respectively. Using experimental and theoretical THz spectroscopy, we elucidate nanoconfinement effects on the H-bond network of stratified water lamellae that are hosted within graphene-based two-dimensional pores. Characteristic confinement-induced changes of the THz response are traced back to the level of structural dynamics, notably distinct resonances due to intralayer and interlayer H-bonds at correspondingly low and high intermolecular stretching frequencies and impact of dangling (free) OH bonds at the water-graphene interface that enormously broaden the librational band in sufficiently narrow pores. The interplay of these molecular effects causes characteristic changes of the THz lineshape upon nanoconfining water.

Refined metadynamics through canonical sampling using time-invariant bias potential: A study of polyalcohol dehydration in hot acidic solutions.

We propose a canonical sampling method to refine metadynamics simulations a posteriori, where the hills obtained from metadynamics are used as a time-invariant bias potential. In this way, the statistical error in the computed reaction barriers is reduced by an efficient sampling of the collective variable space at the free energy level of interest. This simple approach could be useful particularly when two or more free energy barriers are to be compared among chemical reactions in different or competing conditions. The method was then applied to study the acid dependence of polyalcohol dehydration reactions in high-temperature aqueous solutions. It was found that the reaction proceeds consistently via an SN 2 mechanism, whereby the free energy of protonation of the hydroxyl group created as an intermediate is affected significantly by the acidic species. Although demonstration is shown for a specific problem, the computational method suggested herein could be generally used for simulations of complex reactions in the condensed phase.

Quantifying anisotropic dielectric response properties of nanoconfined water within graphene slit pores.

Water presents puzzling properties once it gets confined down to the scale below about one nanometer, in particular its dielectric response becomes highly anisotropic in inhomogeneous environments such as slit pores. Here, we analyze the dielectric response of water within graphene slit pores in different confinement regimes based on molecular dynamics simulations. Our data quantify how the distinctly different parallel (in-plane) and perpendicular (out-of-plane) dielectric profiles change upon two-dimensional confinement from wide pores - featuring bulk-like behavior in between typical interfacial water layers - down to the water bilayer and monolayer limit. In addition, we show that simulating water in such narrow pores requires specific water-graphene interaction parameters different from those usually employed for interfaces.

Nanoconfined Water within Graphene Slit Pores Adopts Distinct Confinement-Dependent Regimes.

In view of the increasing importance of nanoconfined aqueous solutions for various technological applications, it has become necessary to understand how strong confinement affects the properties of water at the level of molecular and even electronic structure. By performing extensive ab initio simulations of two-dimensionally nanoconfined water lamellae between graphene sheets subject to different interlayer spacings, we find new regimes at interlayer distances of 10 Å and less where water can be described neither to behave like interfacial water nor to be bulklike at the level of its H-bonding characteristics and electronic structure properties. It is expected that this finding will offer new opportunities to tune both diffusive and reactive processes taking place in aqueous environments that are strongly confined by chemically inert hard walls.

The reaction mechanism of polyalcohol dehydration in hot pressurized water.

The use of high-temperature liquid water (HTW) as a reaction medium is a very promising technology in the field of green chemistry. In order to fully exploit this technology, it is crucial to unravel the reaction mechanisms of the processes carried out in HTW. In this work, the reaction mechanism of 2,5-hexanediol dehydration in HTW has been studied by means of three different ab initio simulations: the string method, metadynamics and molecular dynamics in real time. It is found that the whole reaction involving protonation, bond exchange and deprotonation occurs in a single step without a stable intermediate. The hydrogen bonded network of the surrounding water has a vital role in assisting an efficient proton relay at the beginning and at the end of the reaction. It is confirmed that the reaction is energetically most favorable in the SN2 pathway with an estimated barrier of 36 kcal mol-1, which explains the high stereoselectivity and the reaction rate observed in experiment. The mechanistic insights provided by our study are relevant for a prominent class of reactions in the context of sustainable biomass processing, namely dehydration reactions of polyalcohol molecules.

The excited-state structure, vibrations, lifetimes, and nonradiative dynamics of jet-cooled 1-methylcytosine.

We have investigated the S0 → S1 UV vibronic spectrum and time-resolved S1 state dynamics of jet-cooled amino-keto 1-methylcytosine (1MCyt) using two-color resonant two-photon ionization, UV/UV holeburning and depletion spectroscopies, as well as nanosecond and picosecond time-resolved pump/delayed ionization measurements. The experimental study is complemented with spin-component-scaled second-order coupled-cluster and multistate complete active space second order perturbation ab initio calculations. Above the weak electronic origin of 1MCyt at 31 852 cm-1 about 20 intense vibronic bands are observed. These are interpreted as methyl group torsional transitions coupled to out-of-plane ring vibrations, in agreement with the methyl group rotation and out-of-plane distortions upon 1ππ∗ excitation predicted by the calculations. The methyl torsion and ν1' (butterfly) vibrations are strongly coupled, in the S1 state. The S0 → S1 vibronic spectrum breaks off at a vibrational excess energy Eexc ∼ 500 cm-1, indicating that a barrier in front of the ethylene-type S1⇝S0 conical intersection is exceeded, which is calculated to lie at Eexc = 366 cm-1. The S1⇝S0 internal conversion rate constant increases from kIC = 2 ⋅ 109 s-1 near the S1(v = 0) level to 1 ⋅ 1011 s-1 at Eexc = 516 cm-1. The 1ππ∗ state of 1MCyt also relaxes into the lower-lying triplet T1 (3ππ∗) state by intersystem crossing (ISC); the calculated spin-orbit coupling (SOC) value is 2.4 cm-1. The ISC rate constant is 10-100 times lower than kIC; it increases from kISC = 2 ⋅ 108 s-1 near S1(v = 0) to kISC = 2 ⋅ 109 s-1 at Eexc = 516 cm-1. The T1 state energy is determined from the onset of the time-delayed photoionization efficiency curve as 25 600 ± 500 cm-1. The T2 (3nπ∗) state lies >1500 cm-1 above S1(v = 0), so S1⇝T2 ISC cannot occur, despite the large SOC parameter of 10.6 cm-1. An upper limit to the adiabatic ionization energy of 1MCyt is determined as 8.41 ± 0.02 eV. Compared to cytosine, methyl substitution at N1 lowers the adiabatic ionization energy by ≥0.32 eV and leads to a much higher density of vibronic bands in the S0 → S1 spectrum. The effect of methylation on the radiationless decay to S0 and ISC to T1 is small, as shown by the similar break-off of the spectrum and the similar computed mechanisms.

Conical Intersection Optimization Using Composed Steps Inside the ONIOM(QM:MM) Scheme: CASSCF:UFF Implementation with Microiterations.

Three algorithms for optimization of minimum energy conical intersections (MECI) are implemented inside an ONIOM(QM:MM) scheme combined with microiterations. The algorithms follow the composed gradient (CG), composed gradient-composed steps (CG-CS), and double Newton-Raphson-composed step (DNR-CS) schemes developed previously for purely QM optimizations. The CASSCF and UFF methods are employed for the QM and MM calculations, respectively. Conical intersections are essential to describe excited state processes in chemistry, including biological systems or functional molecules, and our approach is suitable for large molecules or systems where the excitation is well localized on a fragment that can be treated at the CASSCF level. The algorithms are tested on a set of 14 large hydrocarbons composed of a medium-sized chromophore (fulvene, benzene, butadiene, and hexatriene) derivatized with alkyl substituents. Thanks to the microiteration technique, the number of steps required to optimize the MECI of the large molecules is similar to the one needed to optimize the unsubstituted chromophores at the QM level. The three tested algorithms have a similar performance, although the CG-CS implementation is the most efficient one on average. The implementation can be straightforwardly applied to ONIOM(QM:QM) schemes, and its potential is further demonstrated locating the MECI of diphenyl dibenzofulvene (DPDBF) in its crystal, which is relevant for the aggregation induced emission (AIE) of this molecule. A cluster of 12 molecules (528 atoms) is relaxed during the MECI optimization, with one molecule treated at the QM level. Our results confirm the mechanistic picture that AIE in DPDBF is due to the packing of the molecules in the crystal. Even when the molecules surrounding the excited molecule are allowed to relax, the rotation of the bulky substituents is hindered, and the conical intersection responsible for radiationless decay in solution is not accessible energetically.

Photophysics of fulvene under the non-resonant stark effect. Shaping the conical intersection seam.

We introduce a mechanistic strategy to control the excited state lifetime of fulvene based on shaping the topography of an extended seam of intersection with the non-resonant dynamic Stark effect. Fulvene has a very short excited state lifetime due to an energetically accessible seam of intersection which lies along the methylene torsion coordinate, and the initial decay occurs at the seam segment around the planar conical intersection structure. We have followed a three-step approach to simulate the control. First, we have calculated the effect of a non-resonant electric field on the potential energy surface at the ab initio level, including the field in a self-consistent way. The relative energy of the planar segment of the seam is increased by the non-resonant field. In the second step we simulate the control carrying out MCTDH quantum dynamics propagations under a static non-resonant field to derive the main control mechanisms. At moderately intense fields (epsilon < or = 0.03 a.u.) the decay is faster as compared to the field free case because the vibrational overlap between the excited and ground state vibrational functions is increased. However, at more intense fields (epsilon = 0.04 a.u.) the planar conical intersection is energetically inaccessible and the decay occurs at a slower time scale, at the segment of the seam with more twisted geometries. In the third step, the control over the dynamics is exerted with a non-resonant dynamic field. The acceleration of the decay due to the improved vibrational overlap does not occur, but the decay can be made slower with a dynamic field of 0.08 a.u. The results show the viability of our approach to control the photophysics shaping the topology of the conical intersection seam, and they prove that the extended nature of the seam is crucial for simulating and understanding the control.

Conical Intersection Optimization Based on a Double Newton-Raphson Algorithm Using Composed Steps.

An algorithm for conical intersection optimization based on a double Newton-Raphson step (DNR) has been implemented and tested in 11 cases using CASSCF as the electronic structure method. The optimization is carried out in redundant coordinates, and the steps are the sum of two independent Newton-Raphson steps. The first step is carried out to reach the energy degeneracy and uses the gradient of the energy difference between the crossing states and the so-called branching space Hessian. The second step minimizes the energy in the intersection space and uses the projected excited state gradient and the intersection space Hessian. The branching and intersection space Hessians are obtained with a Broyden-Fletcher-Goldfarb-Shanno update from the gradient difference and projected excited state gradients, respectively. In some cases, mixing of the quasi-degenerate states near the seam causes changes in the direction of the gradient difference vector and induces a loss of the degeneracy. This behavior is avoided switching to a composed step (CS) algorithm [Sicilia et al. J. Chem. Theory Comput.2008, 4, 27], i.e., a hybrid DNR-CS implementation. Compared to the composed gradient (CG) [Bearpark et al. Chem. Phys. Lett.1994, 223, 269] and hybrid CG-CS algorithms, the DNR-CS algorithm reaches the MECI in 30% and 15% less steps, respectively. The improvement occurs mostly because the approach to the seam is more efficient, and a degeneracy threshold of 0.001 hartree is reached at lower energies than in the CG and CG-CS cases.