The Paesani Research Group

Laboratory for Theoretical and Computational Chemistry at UC San Diego  

101. Temperature-dependent vibrational spectra and structure of liquid water from classical and quantum

        simulations with the MB-pol potential energy function. S.K. Reddy, D.R. Moberg, S.C. Straight, F. Paesani,

        J. Chem. Phys. 147, 244504 (2017). [link]  

The structure of liquid water as a function of temperature is investigated through the modeling of infrared and

Raman spectra along with structural order parameters calculated from classical and quantum molecular

dynamics simulations with the MB-pol many-body potential energy function. The magnitude of nuclear

quantum effects is also monitored by comparing the vibrational spectra obtained from classical and centroid

molecular dynamics, both in intensities and peak positions. The observed changes in spectral activities are

shown to reflect changes in the underlying structure of the hydrogen-bond network and are found to be

particularly sensitive to many-body effects in the representation of the electrostatic interactions. Overall,

good agreement is found with the experimental spectra, which provides further evidence for the accuracy

of MB-pol in predicting the properties of water.

100. Ultrafast direct electron transfer at organic semiconductor and metal interfaces. B. Xiang, Y. Li, C.H. Pham,

        F. Paesani, W. Xiong, Science Adv. 3, e1701508 (2017). [link]   

In this collaboration with the Xiong group, we demonstrate conformation-specific electron transfer at

buried interfaces between an organic polymer semiconductor film and a gold substrate by observing the

first dynamical electric-field-induced vibrational sum-frequency generation spectra. The measurements

unequivocally show that, although the gold/polymer interfaces are prepared without deliberate alignment

control, electrons can still be directly transferred from the Fermi level of the gold substrate to the LUMO

of the organic semiconductor. Theoretical calculations performed at the density functional theory level

ascribe the observed direct electron transfer to a sub-ensemble of flat-lying polymer configurations in

which the electronic orbitals are delocalized across the interface. The observation of direct electron

transfer at complex interfaces as well as the insights gained into the relationship between molecular

conformations and electron dynamics will have implications for implementing novel direct electron transfer

in energy materials.

99. Pore breathing of metal-organic frameworks by environmental transmission electron microscopy. L.R. Parents,

      C.H. Pham, J.P. Pattersson, M.S. Denny, Jr., S.M. Cohen, N.C. Gianneschi, F. Paesani, J. Am. Chem. Soc. 139, 13973

      (2017). [link]

In this joint experimental-computational study, we characterize, for the first time, the

"breathing behavior" of metal-organic frameworks at the lattice level through the combination of in

situ environmental transmission electron microscopy (ETEM) and molecular dynamics (MD)

simulations. Our combined approach enables the direct monitoring of the “breathing behavior” of

individual MIL-53(Cr) nanocrystals upon reversible water adsorption and temperature changes. The

ability to characterize structural changes in single nanocrystals and extract lattice level information

through in silico correlation will open the door to fundamental studies of the relationship between pore

size/shape and host-guest interactions in different mesoporous nanomaterials for potential applications

as molecular switches, memory devices, chemical sensors, gas storage materials, and drug delivery


97. Molecular origin of the vibrational spectra of ice Ih. D.R. Moberg, S.C. Straight, C. Knight, F. Paesani,

      J. Phys. Chem. Lett. 8, 2579 (2017). [link]

An unambiguous assignment of the vibrational spectra of ice Ih remains a matter of debate.

This study demonstrates that an accurate representation of many-body interactions between

water molecules, combined with an explicit treatment of nuclear quantum effects through

many-body molecular dynamics (MB-MD), leads to a unified interpretation of the vibrational

spectra of ice Ih in terms of the structure and dynamics of the underlying hydrogen-bond

network. All features of the infrared and Raman spectra in the OH stretching region can be

unambiguously assigned by taking into account both the symmetry and the delocalized nature

of the lattice vibrations as well as the local electrostatic environment experienced by each

water molecule within the crystal. The high level of agreement with experiment raises prospects

for predictive MB-MD simulations that, complementing analogous measurements, will provide

molecular-level insights into fundamental processes taking place in bulk ice and on ice surfaces

under different thermodynamic conditions.

96. Monitoring water clusters "melt" through vibrational spectroscopy. S.E. Brown, A.W. Götz, X. Cheng,

      R.P. Steele, V. Mandelshtam, F. Paesani, J. Am. Chem. Soc. 139, 7082 (2017). [link]   

In this study, state-of-the-art quantum simultions with a many-body water potential energy surface,

which exhibits chemical and spectroscopic accuracy, ar carried out to monitor the microscopic

melting of the water hexamer through the analysis of vibrational spectra and appropriate structural

order parameters as a function of temperature. The water hexamer is specifically chosen as a case

study due to the central role of this cluster in the molecular-level understanding of hydrogen bonding

in water. Besides being in agreement with the experimental data available for selected isomers at

very low temperature, the present results provide quantitative insights into the interplay between

energetic, entropic, and nuclear quantum effects on the evolution of water clusters from “solid-like”

to “liquid-like” structures. This study thus demonstrates that computer simulations can now bridge

the gap between measurements currently possible for individual isomers at very low temperature

and observations of isomer mixtures at ambient conditions.

95. Many-body interactions in ice. C.H. Pham, S.K. Reddy, K. Chen, C. Knight, F. Paesani,

      J. Chem. Theory Comput. 13, 1778 (2017). [link]

We investigate many-body effects in ice through a systematic analysis of the lattice energies of several

proton ordered and disordered phases which are calculated with different flexible water models, ranging

from pairwise additive (q-TIP4P/F) to polarizable (TTM3-F and AMOEBA) and explicit many-body (MB-pol)

potential energy functions. Comparisons with available experimental and diffusion Monte Carlo data

emphasize the importance of an accurate description of the individual terms of the many-body expansion

of the interaction energy between water molecules for the correct prediction of the energy ordering of the

ice phases. Further analysis of the MB-pol results in terms of fundamental energy contributions

demonstrates that the differences in lattice energies between different ice phases depend sensitively on the

subtle balance between short-range two-body and three-body interactions, many-body induction, and

dispersion energy. This study provides further support for the accuracy of MB-pol in representing the properties

of water from the gas to the condensed phase.

94. Sodium – carboxylate contact ion pair formation induces stabilization of palmitic acid monolayers at high pH.

      E.M. Adams, B.A. Wellen, R. Thiraux, S.K. Reddy, A.S. Vidalis, F. Paesani, H.C. Allen,

      Phys. Chem. Chem. Phys. 19, 10481 (2017). [link]

In this collaborative study with the Allen group (Ohio State University), we investigate the effect of pH

and salt on the stability and organization of a palmitic acid (PA) monolayer by surface vibrational

spectroscopy and molecular dynamics simulations. Results indicate that alkyl chain packing becomes

more disordered as the carboxylic headgroup becomes deprotonated. This is associated with packing

mismatch of charged and neutral species as charged headgroups penetrate deeper into the solution

phase. At pH 10.7, when the monolayer is ~99% deprotonated, palmitate (PA) molecules desorb and

solubilize into the bulk solution where they form micellar structures. Yet, addition of 100 mM NaCl to

the bulk solution is found to drive PA molecules to the aqueous surface. Free energy calculations show

that PA molecules become stabilized within the interface with increasing NaCl concentration. Formation

of contact –COO:Na+ pairs alters the hydration state of PA headgroups, thus increasing the surface propensity.

© Paesani Research Group. All rights reserved.

Publications 2017

92. Ice nucleation efficiency of hydroxylated organic surfaces is controlled by their structural fluctuations and

      mismatch to ice. Y. Qiu, N. Odendahl, A. Hudait, R.H. Mason, A.K. Bertram, F. Paesani, P.J. DeMott, V. Molinero,

      J. Am. Chem. Soc. 139, 3052 (2017). [link]  

In this collaborative work led by the Molinero group (University of Utah) we use molecular dynamics

simulations and laboratory experiments to investigate the relationship between the structure and

fluctuations of hydroxylated organic surfaces and the temperature at which they nucleate ice. We find

that these surfaces order interfacial water to form domains with ice-like order that are the birthplace

of ice. Both mismatch and fluctuations decrease the size of the pre-ordered domains and monotonously

decrease the ice freezing temperature. The simulations indicate that fluctuations depress the freezing

efficiency of monolayers of alcohols or acids to half the value predicted from lattice mismatch alone.

The model captures the experimental trend in freezing efficiencies as a function of chain length, and

predicts that alcohols have higher freezing efficiency than acids of the same chain length.

93. Computational exploration of the water concentration-dependence of the proton transport in the porous

      UiO-66(Zr)-(CO2H)2 metal. D. Damasceno Borges, R. Semino, S. Devaoutour-Vinot, H. Jobic, F. Paesani, G. Maurin,

      Chem. Mater. 29, 1569 (2017). [link]

In this study, we perform aMS-EVB3 molecular dynamics simulations to reveal, at the molecular level,

the structure, thermodynamics and dynamics of the hydrated proton in this 3D-cages MOF as a function

of the water loading. It is found that the most stable proton solvation structure corresponds to a H7O3+ cation

and that a transition between this complex and a Zundel cation likely governs the proton transport in

this MOF occurring via a Grotthus-type mechanism. It is further shown that the formation of a H2O

hydrogen-bonded bridge that connects the cages only occurs at high water concentration and this creates

a path allowing the excess proton to jump from one cage to another. This leads to a faster self-diffusivity

of proton at high water concentration, thereby supporting the increase of the proton conductivity with the

water loading as experimentally evidenced.  

98. Toward chemical accuracy in the description of ion–water interactions through many-body representations.     

       Alkali-water dimer potential energy surfaces. M. Riera, N. Mardirossian, P. Bajaj, A.W. Götz, F. Paesani,

      J. Chem. Phys. 147, 161715 (2017). [link]

This study presents the extension of the MB-nrg (Many-Body energy) theoretical/computational

framework of transferable potential energy functions (PEFs) for molecular simulations of alkali metal

ion-water systems. Specific focus is on the MB-nrg two-body terms describing the full-dimensional

potential energy surfaces of the M+(H2O) dimers, where M+ = Li+, Na+, K+, Rb+, and Cs+. The

accuracy of the MB-nrg PEFs is systematically assessed through an extensive analysis of interaction

energies, structures, and harmonic frequencies for all five M+(H2O) dimers. In all cases, the MB-nrg

PEFs are shown to be superior to both polarizable force fields and DFT models. As previously

demonstrated for halide-water dimers, the MB-nrg PEFs achieve higher accuracy by correctly describing

short-range quantum-mechanical effects associated with electron density overlap as well as long-range

electrostatic many-body interactions.

102. Making ice from stacking-disordered crystallites. F. Paesani, Chem. 3, 926 (2017). [link]  

In this Preview article, we highlight a recent study by the Molinero group that has recently appeared in the

literature [Nature 551, 218, (2017)]. In that study, Lupi et al. used computer simulations to elucidate the

molecular mechanisms of ice nucleation. Their simulations demonstrate that the initial crystallites are stacking

disordered due to entropy gains. By analyzing ~30,000 MD nucleation trajectories Lupi et al. determined that

ice nucleation proceeds through a minimum free-energy path from the liquid to the top of the free-energy

barrier and can be effectively described by following the size evolution of the ice crystallite. Both findings

are consistent with CNT predictions. However, the simulations also show that stacking disordered nuclei are

more stable than hexagonal nuclei. The stabilization is due a large entropic gain associated with mixing cubic

and hexagonal layers, which makes stacking-disordered ice the stable phase for crystallites with up to at

least ~100,000 water molecules. These results contradict CNT’s assumption that the driving force for

homogenous ice nucleation is the free-energy difference between ice Ih and liquid water.