12 research outputs found
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 tech- nology 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 mecha- nism of 2,5-hexanediol dehydration in HTW has been studied by means of three different ab initio simulations: string method, metadynamics and molecular dynamics in real time. It is found that the whole reaction involving the protonation, bond exchange and the deprotonation occurs in a single step without a stable intermediate. The hydrogen bonded network of 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, 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
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 SN2 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
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 timeresolved
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 ν′1 (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 mechanismsThis research has been supported by the Schweiz. Nationalfonds (Grant Nos. 121993 and 132540), the Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR) from Catalonia (Spain) (Grant No. 2014SGR1202), the Ministerio de Economía y Competividad (MINECO) from Spain (Grant No. CTQ2015-69363-P), and the National Natural Science Foundation of China (Grant No. 21303007
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 timeresolved
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 ν′1 (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 mechanismsThis research has been supported by the Schweiz. Nationalfonds (Grant Nos. 121993 and 132540), the Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR) from Catalonia (Spain) (Grant No. 2014SGR1202), the Ministerio de Economía y Competividad (MINECO) from Spain (Grant No. CTQ2015-69363-P), and the National Natural Science Foundation of China (Grant No. 21303007
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
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
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.<i> J. Chem. Theory Comput.</i> <b>2008</b>, <i>4</i>, 27], i.e., a hybrid DNR-CS implementation. Compared to the composed
gradient (CG) [Bearpark et al. <i>Chem. Phys. Lett.</i> <b>1994</b>, <i>223</i>, 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
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