19 research outputs found
Molecular Dynamics of Photoinduced Reactions of Acrylic Acid: Products, Mechanisms, and Comparison with Experiment
The photochemistry
of acrylic acid is of considerable atmospheric
importance. However, the mechanisms and the time scales of the reactions
involved are unknown. In this work, the products, yields, and reaction
pathways of acrylic acid photochemistry are investigated theoretically
by molecular dynamics simulations on the ππ* excited state.
Two methods were used to describe the excited state: the semiempirical
OM2/MRCI and the ab initio ADC(2). Over 100 trajectories were computed
with each method. A rich variety of reaction channels including mechanisms,
time scales, and yields are predicted for the single potential energy
surface used. Main findings include: (1) Products predicted by the
calculations are in good agreement with experiments; (2) ADC(2) seems
to validate OM2/MRCI predictions on main aspects of mechanisms, but
not on time scales. It is concluded that both semiempirical and ab
initio molecular dynamics simulations have useful advantages for the
description of photochemical dynamics of carboxylic acids
Approximate Quantum Dynamics using Ab Initio Classical Separable Potentials: Spectroscopic Applications
Algorithms for quantum molecular
dynamics simulations that directly
use ab initio methods have many potential applications. In this article,
the ab initio classical separable potentials (AICSP) method is proposed
as the basis for approximate algorithms of this type. The AICSP method
assumes separability of the total time-dependent wave function of
the nuclei and employs mean-field potentials that govern the dynamics
of each degree of freedom. In the proposed approach, the mean-field
potentials are determined by classical ab initio molecular dynamics
simulations. The nuclear wave function can thus be propagated in time
using the effective potentials generated “on the fly”.
As a test of the method for realistic systems, calculations of the
stationary anharmonic frequencies of hydrogen stretching modes were
carried out for several polyatomic systems, including three amino
acids and the guanine–cytosine pair of nucleobases. Good agreement
with experiments was found. The method scales very favorably with
the number of vibrational modes and should be applicable for very
large molecules, e.g., peptides. The method should also be applicable
for properties such as vibrational line widths and line shapes. Work
in these directions is underway
Autocorrelation of electronic wave-functions: a new approach for describing the evolution of electronic structure in the course of dynamics
<p>We introduce a new approach for analysing changes in electronic structure in the course of <i>ab initio</i> molecular dynamics simulations. The analysis is based on the time autocorrelation function of the many-body electronic wave-function. The approach facilitates the interpretation of dynamical events that may not be easily revealed by consideration of nuclear configurations alone. We apply the method to several illustrative examples: the shared proton vibration in the F<sup>−</sup>(H<sub>2</sub>O) complex, representing changes in strength of non-covalent interactions; proton transfer in the water dimer cation, as an example for chemical reactions in weakly bound systems; and the intramolecular proton transfer in malonaldehyde. In all cases, we observe distinct features in the time autocorrelation function when chemical changes occur. The autocorrelation function serves as an effective reaction coordinate, incorporating all degrees of freedom, including electronic ones. The method is also sensitive to changes in the electronic wave-function not accompanied by significant nuclear motions.</p
Photochemical Reactions of Cyclohexanone: Mechanisms and Dynamics
Photochemistry
of carbonyl compounds is of major importance in
atmospheric and organic chemistry. The photochemistry of cyclohexanone
is studied here using on-the-fly molecular dynamics simulations on
a semiempirical multireference configuration interaction potential-energy
surface to predict the distribution of photoproducts and time scales
for their formation. Rich photochemistry is predicted to occur on
a picosecond time scale following the photoexcitation of cyclohexanone
to the first singlet excited state. The main findings include: (1)
Reaction channels found experimentally are confirmed by the theoretical
simulations, and a new reaction channel is predicted. (2) The majority
(87%) of the reactive trajectories start with a ring opening via C–C<sub>α</sub> bond cleavage, supporting observations of previous
studies. (3) Mechanistic details, time scales, and yields are predicted
for all reaction channels. These benchmark results shed light on the
photochemistry of isolated carbonyl compounds in the atmosphere and
can be extended in the future to photochemistry of more complex atmospherically
relevant carbonyl compounds in both gaseous and condensed-phase environments
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Proton Transfer in Mixed Clusters of Methanesulfonic Acid, Methylamine, and Oxalic Acid: Implications for Atmospheric Particle Formation
Understanding the
properties of atmospheric particles made of several
components is a very challenging problem. In this paper, we perform
quantum chemical calculations for small multicomponent clusters of
atmospheric relevance that incorporate methanesulfonic acid (MSA),
methylamine (MA), oxalic acid (OxA), and water (H<sub>2</sub>O). Potential
correlations between theoretical predictions of proton transfer in
the small clusters and findings of recent experiments on formation
of particles of detectable sizes (>2 nm) from the same components
are studied. It is proposed that proton transfer from the acid to
the amine in the 1:1 clusters correlates with experiments on particle
formation in systems, such as MSA-MA and MSA-MA-OxA. In the case of
OxA + MA, which has been observed to give few particles, proton transfer
does not occur for the 1:1 cluster but does for the 2:2 cluster. Adding
H<sub>2</sub>O to OxA-MA promotes the occurrence of proton transfer,
and corresponding particles are slightly enhanced. The partial charge
on the MA component increases by adding OxA or H<sub>2</sub>O to MSA-MA,
which is correlated with enhanced particle formation compared to MSA-MA
alone. Ab initio molecular dynamics simulations show that proton transfer
at room temperature (<i>T</i> = 298 K) and high temperature
(<i>T</i> = 500 K) is little affected compared with the
equilibrium structure (<i>T</i> = 0 K). These results suggest
that small cluster calculations may be useful in predicting the formation
of multicomponent particles in the atmosphere
Monosaccharide-Water Complexes: Vibrational Spectroscopy and Anharmonic Potentials
Ab initio vibrational self-consistent field (VSCF) calculations
are used to predict the vibrational spectra of an extended series
of monosaccharide·D<sub>2</sub>O complexes, including glucose,
galactose, mannose, xylose, and fucose in their α and β
anomeric forms, and compared with recently published experimental
data for their (phenyl-tagged) complexes. Anharmonic VSCF-PT2 frequencies
are calculated directly, using ab initio hybrid HF/MP2 potentials,
to assess their accuracy in reproducing the vibrational anharmonicities
and provide a more rigorous basis for vibrational and structural assignments.
The average discrepancies between the calculated and experimental
frequencies are ∼1.0–1.5%, and the first-principles
spectroscopic calculations, free of any empirical scaling, yield results
of high accuracy. They encourage confidence in their future application
to the assignment of other carbohydrate systems, both free and complexed,
and an improved understanding of their intra- and intermolecular carbohydrate
interactions
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The Role of Oxalic Acid in New Particle Formation from Methanesulfonic Acid, Methylamine, and Water
Atmospheric
particles are notorious for their effects on human
health and visibility and are known to influence climate. Though sulfuric
acid and ammonia/amines are recognized as main contributors to new
particle formation (NPF), models and observations have indicated that
other species may be involved. It has been shown that nucleation from
methanesulfonic acid (MSA) and amines, which is enhanced with added
water, can also contribute to NPF. While organics are ubiquitous in
air and likely to be involved in NPF by stabilizing small clusters
for further growth, their effects on the MSA–amine system are
not known. This work investigates the effect of oxalic acid (OxA)
on NPF from the reaction of MSA and methylamine (MA) at 1 atm and
294 K in the presence and absence of water vapor using an aerosol
flow reactor. OxA and MA do not efficiently form particles even in
the presence of water, but NPF is enhanced when adding MSA to OxA-MA
with and without water. The addition of OxA to MSA-MA mixtures yields
a modest NPF enhancement, whereas the addition of OxA to MSA-MA-H<sub>2</sub>O has no effect. Possible reasons for these effects are discussed
Formation of Chlorine in the Atmosphere by Reaction of Hypochlorous Acid with Seawater
The highly reactive dihalogens play
a significant role
in the oxidative
chemistry of the troposphere. One of the main reservoirs of these
halogens is hypohalous acids, HOX, which produce dihalogens in the
presence of halides (Y–), where X, Y = Cl, Br, I.
These reactions occur in and on aerosol particles and seawater surfaces
and have been studied experimentally and by field observations. However,
the mechanisms of these atmospheric reactions are still unknown. Here,
we establish the atomistic mechanism of HOCl + Cl– → Cl2 + OH– at the surface of
the water slab by performing ab initio molecular dynamics (AIMD) simulations.
Main findings are (1) This reaction proceeds by halogen-bonded complexes
of (HOCl)···(Cl–)aq surrounded
with the neighboring water molecules. (2) The halogen bonded (HOCl)···(Cl–)aq complexes undergo charge transfer from
Cl– to OH– to form transient Cl2 at neutral pH. (3) The addition of a proton to one proximal
water greatly facilitates the Cl2 formation, which explains
the enhanced rate at low pH
Formation of Chlorine in the Atmosphere by Reaction of Hypochlorous Acid with Seawater
The highly reactive dihalogens play
a significant role
in the oxidative
chemistry of the troposphere. One of the main reservoirs of these
halogens is hypohalous acids, HOX, which produce dihalogens in the
presence of halides (Y–), where X, Y = Cl, Br, I.
These reactions occur in and on aerosol particles and seawater surfaces
and have been studied experimentally and by field observations. However,
the mechanisms of these atmospheric reactions are still unknown. Here,
we establish the atomistic mechanism of HOCl + Cl– → Cl2 + OH– at the surface of
the water slab by performing ab initio molecular dynamics (AIMD) simulations.
Main findings are (1) This reaction proceeds by halogen-bonded complexes
of (HOCl)···(Cl–)aq surrounded
with the neighboring water molecules. (2) The halogen bonded (HOCl)···(Cl–)aq complexes undergo charge transfer from
Cl– to OH– to form transient Cl2 at neutral pH. (3) The addition of a proton to one proximal
water greatly facilitates the Cl2 formation, which explains
the enhanced rate at low pH
NO<sub><i>x</i></sub> Reactions on Aqueous Surfaces with Gaseous HCl: Formation of a Potential Precursor to Atmospheric Cl Atoms
Chlorine atoms are highly reactive free radicals known
to catalyze
ozone depletion in the stratosphere and organic oxidation in the troposphere.
They are readily produced photolytically upon irradiation of some
stable Cl containing species, for instance, nitrosyl chloride, ClNO.
We predict the formation of ClNO using ab initio molecular dynamics
(AIMD) simulations of an NO<sub>2</sub> dimer on the surface of a
thin film of water upon which gaseous HCl impinges. The reactant is
chloride ion formed when HCl ionizes on the water film. The same mechanism
for ClNO production may occur in humid environments when ONONO<sub>2</sub> (the asymmetric NO<sub>2</sub> dimer examined here) comes
in contact with either HCl or sea salt. The film of water serves to
(1) stabilize ONONO<sub>2</sub> on the film surface so that it is
localized and physically accessible for reaction, (2) provide the
medium to ionize HCl, and (3) activate ONONO<sub>2</sub> making it
more susceptible to nucleophilic attack by chloride. This substitution/elimination
mechanism is new for NO<sub><i>x</i></sub> chemistry on
thin water films and could not be derived from studies on small clusters