The Paesani Research Group

Laboratory for Theoretical and Computational Chemistry at UC San Diego  

127. Halogen bonding in UiO-66 frameworks promotes superior chemical warfare agent simulant degradation.

        M. Kalaj, M.R.. Momeni, K.C. Bents, K.S. Barcus, J.M. Palomba, F. Paesani, S.M. Cohen, Chem. Commun. 55, 3481,

        (2019). [link]

In this study, a series of halogenated UiO-66 derivatives was synthesized and analyzed

for the breakdown of the CWA simulant dimethyl-4- nitrophenyl phosphate (DMNP) to

analyze ligand effects. UiO-66-I degrades DMNP at a rate four times faster than the

most active previously reported MOFs. MOF defects were quantified and ruled out as

a cause for increased activity. Theoretical calculations suggest the enhanced activity

of UiO-66-I originates from halogen bonding of the iodine atom to the phosphoester

linkage allowing for more rapid hydrolysis of the P-O bond.

© Paesani Research Group. All rights reserved.

Publications 2019

122. Water structure at the interface of alcohol monolayers as predicted by computational sum-frequency

        generation spectroscopy. D.R. Moberg, Q. Li, S.K. Reddy, F. Paesani, J. Chem. Phys. 150, 034701 (2019). [link]

In this study, we investigate the structure of water at the interface of three long- chain alcohol monolayers

differing in alkyl chain length through molecular dynamics simulations combined with modeling of vibrational

sum frequency generation (vSFG) spectra. The effects of alkyl chain parity on interfacial water is examined

through extensive analysis of structural properties, hydrogen bonding motifs, and spectral features. Besides

providing molecular-level insights into the structure of interfacial water, this study also suggests that, by

enabling direct comparisons with experimental vSFG spectra, computational spectroscopy may be used to

test and validate force fields commonly used in biomolecular simulations. The results presented here can

thus serve as benchmarks for both further investigations to characterize ice nucleation induced by alcohol

monolayers and refinement of popular biomolecular force fields.

123. Assessment of density functional theory in predicting interaction energies between water and polycyclic

        aromatic hydrocarbons: From water on benzene to water on graphene. A.O. Ajala, V. Voora, N. Mardirossian,

        F. Furche, F. Paesani, J. Chem. Theory Comput. 15, 2359 (2019). [link]

The interaction of water with polycyclic aromatic hydrocarbons, from benzene to graphene, is investigated using

various DFT models, including GGA, meta-GGA, and hybrid functionals. The accuracy of the different functionals

is assessed through comparisons with RPA, DMC, and L-CCSD(T) data. Relatively large variations are found

in the interaction energies predicted by different DFT models, with B97M-rV and ωB97M-V providing nearly

quantitative agreement with the L-CCSD(T) values available for the water on benzene, coronene, and

circumcoronene which, in turn, are within ~1 kcal/mol of the corresponding RPA and DMC values. ALMO-EDA

results indicate that electrostatics and dispersion are the dominant contributions to the interaction energies.

Importantly, water-graphene interaction energies calcu- lated with the B97M-rV functional appear to deviate

by more than 1 kcal/mol from the available RPA and DMC values.

124. Many-body effects determine the local hydration structure of Cs+ in solution. D. Zhuang, M. Riera,

        G.K. Schenter, J.L. Fulton, F. Paesani, J. Phys. Chem. Lett. 10, 406 (2019). [link]

A systematic analysis of the hydration structure of Cs+ ions in solution is derived from simulations carried out

using a series of molecular models built upon a hierarchy of approximate representations of many-body effects

in ion–water interactions. It is found that a pairwise-additive model, commonly used in biomolecular simulations,

provides poor agreement with experimental X-ray spectra, indicating an incorrect description of the underlying

hydration structure. Although the agreement with experiment im- proves in simulations with a polarizable model,

the predicted hydration structure is found to lack the correct sequence of water shells. Progressive inclusion of

explicit many-body effects in the representation of Cs+–water interactions as well as account for nuclear quantum

effects is shown to be necessary for quantitatively reproducing the experimental X-ray spectra. Besides

emphasizing the importance of many-body effects, these results suggest that molecular models rigorously

derived from many-body expansions hold promise for realistic simulations of aqueous solutions.

125. On the nature of halide-water interactions: Insights from many-body representations and density functional

        theory. B.B. Bizzarro, C.K. Egan, F. Paesani, J. Comp. Theory. Comput. 15, 2983 (2019). [link]

Interaction energies of X(H2O) and X(H2O)2 complexes, with X = F, Cl, Br, and I, are investigated using

various many-body models and exchange-correlation (XC) functionals selected across the hierarchy of

density functional theory (DFT) approximations. Analysis of the results obtained with the many-body models

demonstrates the need to capture important close-range interactions in the regime of large intermolecular

orbital overlap, such as charge transfer and charge penetration. Decompositions of interaction energies

carried out with the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) method

demonstrate that permanent and inductive electrostatic energies are accurately reproduced by all classes of

XC functionals, while significant variance is found for charge transfer energies predicted by different XC

functionals. The sum of Pauli repulsion and dispersion energies are the most varied among the XC functionals,

but it is found that a correspondence between the interaction energy and the ALMO EDA total frozen energy

may be used to determine accurate estimates for these contributions.

126. Ion-mediated hydrogen-bond rearrangement through tunneling in the iodide–dihydrate complex.

        P. Bajaj, J.O. Richardson, F. Paesani, Nat. Chem. 11, 367 (2019). [link]

A microscopic picture of hydrogen-bond structure and dynamics in ion hydration shells remains elusive.

In this study, we use state-of-the-art quantum dynamics simulations to provide evidence for tunneling in

hydrogen-bond rearrangements in the iodide–dihydrate complex and show that it can be controlled

through isotopic substitutions. We find that the iodide ion weakens the neighboring water–water

hydrogen bond, leading to faster water reorientation than in the analogous water trimer. These faster

dynamics, which are apparently at odds with the slowdown observed in the first hydration shell of iodide

in solution, can be traced back to the presence of a free OH bond in the iodide–dihydrate complex,

which effectively triggers the overall structural rearrangements within it. Besides providing indirect

support for co-operative hydrogen-bond dynamics in iodide solutions, the analysis presented here

suggests that iodide ions may accelerate hydrogen-bond rearrangements at aqueous interfaces, where

neighboring water molecules can be undercoordinated.

128. Halide ion micro-hydration: Structure, energetics and spectroscopy of small halide–water clusters.

        P. Bajaj, M. Riera, J.K. Lin, Y.E. Mendoza Montijo, J. Gazca, F. Paesani, J. Phys. Chem. A 123, 2843 (2019). [link]

Replica exchange molecular dynamics simulations and vibrational spectroscopy calculations are performed using

halide-water many-body potential energy functions to provide a bottom-up analysis of the structures, energetics,

and hydrogen-bonding arrangements in X(H2O)n=3−6 clusters, with X = F, Cl, Br, and I. Independently of the cluster

size, it is found that all four halides prefer surface-type structures in which they occupy one of the vertices in the

underlying three-dimensional hydrogen-bond networks. For fluoride-water clusters, this is in contrast with previous

reports suggesting that fluoride prefers interior-type arrangements, where the ion is fully hydrated. These differences

can be ascribed to the variability in how various molecular models are capable to reproduce the subtle interplay

between halide-water and water-water interactions. Our results thus emphasize the importance of a correct

representation of individual many-body contributions to the molecular interactions for a quantitative description

of halide ion hydration.

129. Specific ion effects in hydrogen-bond rearrangements in halide‑dihydrate complexes. P. Bajaj, D. Zhuang,

        F. Paesani, J. Phys. Chem. Lett. 10, 2823 (2019). [link]

Small aqueous ionic clusters represent ideal systems to investigate the microscopic H-bonding structure and

dynamics in ion hydration shells. In this context, halide-dihydrate complexes are the smallest systems where the

interplay between halide–water and water–water interactions can be studied simultaneously. Here, quantum

molecular dynamics simulations unravel specific ion effects on the temperature-dependent structural transition

in X(H2O)2 complexes (X = Cl, Br and I) which is induced by the breaking of the water–water hydrogen bond.

A systematic analysis of the H-bonding rearrangements at low temperature provides fundamental insights into

the competition between halide–water and water–water interactions depending on the properties of the halide

ion. While the halide–water H-bond strength decreases going from Cl(H2O)2 to I(H2O)2, the opposite trend in

observed in the strength of the water–water H-bond, suggesting that nontrivial many-body effects may also be

at play in the hydration shells of halide ions in solution, especially in frustrated systems (e.g., interfaces) where

the water molecules can have dangling OH bonds.

130. Water is not a dynamic polydisperse branched polymer. T. Head-Gordon, F. Paesani, Proc. Natl. Acad. Sci. U.S.A.

         116, 13169 (2019). [link]

In PNAS, Naserifar and Goddard report that their RexPoN water model under ambient conditions comprises a

“dynamic polydisperse branched polymer,” which they speculate explains the existence of the liquid–liquid critical

point (LLCP) in the supercooled region. The observable they rely on to support this is the oxygen–oxygen radial

distribution function, gOO, from a dated neutron scattering experiment. Although it is well known that neutron scattering

is almost exclusively sensitive to hydrogen correlations, and gOO is more reliably obtained from X-ray scattering, they

make the unsupported statement that “the most reliable gOO curve is neutron where there is no inference from

electrons”. However, two X-ray gOO curves in figure 1B of Naserifar and Goddard paper are from a joint neutron X-ray

analysis and neutron scattering study. Given the importance that Naserifar and Goddard place on gOO, it is evident

that their RexPoN model is in disagreement with the most reliable estimate of X-ray.

131. Chemical accuracy in modeling halide ion hydration from many-body representations. F. Paesani, P. Bajaj,

        M. Riera, Adv. Phys. X 4, 1631212 (2019). [link]

Despite the key role that ionic solutions play in several natural and industrial processes, a unified, molecular-level

understanding of how ions affect the structure and dynamics of water across different phases remains elusive. In this

context, computer simulations can provide new insights that are difficult, if not impossible, to obtain by other means.

However, the predictive power of a computer simulation directly depends on the level of “realism” that is used to

represent the underlying molecular interactions. Here, we report a systematic analysis of many-body effects in

halide-water clusters and demonstrate that the recently developed MB-nrg full-dimensional many-body potential

energy functions achieve high accuracy by quantitatively reproducing the individual terms of the many-body expansion

of the interaction energy, thus opening the door to realistic computer simulations of ionic solutions.

132. Low-order many-body interactions determine the local structure of liquid water. M. Riera, E. Lambros,

        T.T. Nguyen, A.W. Götz, F. Paesani, Chem. Sci. 10, 8211 (2019). [link]

Despite its apparent simplicity, water displays unique behavior across the phase diagram which is strictly related to

the ability of the water molecules to form dense, yet dynamic, hydrogen-bond networks that continually fluctuate in

time and space. The competition between different local hydrogen-bonding environments has been hypothesized as

a possible origin of the anomalous properties of liquid water. Through a systematic application of the many-body

expansion of the total energy, we demonstrate that the local structure of liquid water at room temperature is

determined by a delicate balance between two-body and three-body energies, which is further modulated by

higher-order many-body effects. Besides providing fundamental insights into the structure of liquid water, this analysis

also emphasizes that a correct representation of many-body effects requires sub-chemical accuracy that is nowadays

only achieved by many-body models rigorously derived from the many-body expansion of the total energy, which

thus hold great promise for shedding light on the molecular origin of the anomalous behavior of liquid water.

133. A ligand field molecular mechanics study of CO2-induced breathing in the metal–organic framework DUT-8(Ni).

        P. Melix, F. Paesani, T. Heine, Adv. Theory Simul. 1900098 (2019). [link]

Flexible metal–organic Frameworks (MOFs) are an interesting class of materials due to their diverse

properties. One representative of this class is the layered-pillar MOF DUT-8(Ni). This MOF consists

of Ni2 paddle wheels interconnected by naphthalene dicarboxylate linkers and dabco pillars

(Ni2(ndc)2(dabco), ndc = 2,6-naphthalene–dicarboxylate, dabco = 1,4-diazabicyclo-[2.2.2]-octane).

DUT-8(Ni) undergoes a volume change of over 140% upon adsorption of guest molecules. Herein,

a ligand field molecular mechanics (LFMM) study of the CO2-induced flexibility of DUT-8(Ni) is

presented. LFMM is able to reproduce experimental and DFT structural features as well as properties

that require large simulation cells. It is shown that the transformation energy from a closed to open

state of the MOF is overcompensated fivefold by the host–guest interactions. Structural characteristics

of the MOF explain the shape of the energy profile at different loading states and provide useful

insights to the interpretation of previous experimental results.

134. Hydrogen bonding structure of confined water templated by a metal-organic framework with open metal sites.

        A.J. Rieth, K.M. Hunter, M. Dinča, F. Paesani, Nat. Commun. 10, 4771 (2019). [link]

In this study, we combine infrared spectroscopy and advanced molecular dynamics simulations to probe

the structure of confined water as a function of relative humidity within a metal-organic framework

containing cylindrical pores lined with an ordered array of cobalt open coordination sites. Building upon

the quantitative agreement between experimental and theoretical spectra, we demonstrate that water at

low relative humidity initially binds to the open metal sites and subsequently forms disconnected

one-dimensional chains of hydrogen-bonded water molecules bridging between the cobalt sites. Upon

further increase in relative humidity, these water chains nucleate pore filling, with water molecules

occupying the entire pore interior before the relative humidity reaches 30%. Systematic analysis of the

rotational and translational dynamics indicates heterogeneity in this pore-confined water, with water

molecules displaying distinct levels of mobility as a function of the distance from the pore surface.

135. Assessing many-body effects in water self-ions. II. H3O+(H2O)n clusters. C.K. Egan, F. Paesani, J. Chem. Theory

       Comput. 15, 4816 (2019). [link]

The importance of many-body effects in the hydration of the hydronium ion (H3O+) is investigated through

a systematic analysis of the many-body expansion of the interaction energy carried out at the coupled

cluster level of theory for the low-lying isomers of H3O+(H2O)n clusters with n = 1 − 5. This is accomplished

by partitioning individual fragments extracted from the whole clusters into “groups” that are classified by

both the number of H3O+ and water molecules and the H-bonding connectivity within a given fragment.

With the aid of the absolutely localized molecular orbital energy decomposition analysis, this structure-based

partitioning is found to largely correlate with the character of different many-body interactions. This analysis

emphasizes the importance of a many-body representation of inductive electrostatics and charge transfer

in modeling the hydration of an excess proton in water. The comparison between the reference coupled

cluster many-body interaction terms with the corresponding values obtained with various DFT models

demonstrates that many functionals yield an unbalanced treatment of the H3O+(H2O)n configuration space.

136. The end of ice I. D.R. Moberg, D. Becker, C.W. Dierking, F. Zurheide, B. Bandow, U. Buck, A. Hudait, V. Molinero,

        F. Paesani, T. Zeuch, Proc. Natl. Acad. Sci. U.S.A. 116, 24413 (2019). [link]

The appearance of ice I in the smallest possible clusters and the naure of its phase coexistence with liquid water

could not thus far be unravelled. The experimental and theoretical infrared spectroscopic and free energy results

of this work show the emergence of the characteristic hydrogen bonding pattern of ice I in clusters containing

only around 90 water molecules. The onset of crystallization is accompanied by an increase of surface oscillator

intensity with decreasing surface to volume ratio, a new spectral indicator of nanoscale crystallinity of water.

In the size range from 90 to 150 water molecules, we observe mixtures of largely crystalline and purely

amorphous clusters. Our analysis suggests that the liquid-ice I transition in clusters loses its sharp first-order

character at the end of the crystalline size regime and occurs over a range of temperatures through heterophasic

oscillations in time, a process without analog in bulk water. These results can be significant to understand the

state of water confined in proteins and other materials.