Publications

Published articles and preprints

(Co-first authors are marked by †)

15) Nuclear quantum effects and the Grotthuss mechanism dictate the pH of liquid water

S. Dasgupta*,G. Cassone and F. Paesani*.  ChemRxiv (2024) link

Water’s ability to autoionize into hydronium and hydroxide ions dictates the acidity or basicity of aqueous solutions, influencing the reaction pathways of many chemical and biochemical processes. In this study, we determine the molecular mechanisms of the autoionization process by leveraging both the computational efficiency of a deep neural network potential trained on highly accurate data calculated within density-corrected density functional theory and the ability of enhanced sampling techniques to ensure a comprehensive exploration of the underlying multidimensional free- energy landscape. By properly accounting for nuclear quantum effects, our simulations provide an accurate estimate of autoionization constant of liquid water (Kw = 1.23 × 10e−14 ), offering the first realistic molecular-level picture of the autoionization process and emphasizing its quantum-mechanical nature. Importantly, our simulations highlight the central role played by the Grotthuss mechanism in stabilizing solvent-separated ion pair configurations, revealing its profound impact on acid/base equilibria in aqueous environments.

14) Eliminating imaginary vibrational frequencies in quantum-chemical cluster models of enzymatic active sites

 P. Bowling, S.Dasgupta and J.M. Herbert*. J. Chem. Inf. Model. 64, 3912 (2024) link

In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery of the model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or “coordinate-lock” approach is commonly employed but leads to undesirable artifacts in the form of small imaginary frequencies. These preclude evaluation of finite-temperature free-energy corrections, limiting thermochemical calculations to enthalpies only. Full-dimensional vibrational frequency calculations are possible by replacing the fixed-atom constraints with harmonic confining potentials. Here, we compare that approach to an alternative strategy in which fixed-atom contributions to the Hessian are simply omitted. While the latter strategy does eliminate imaginary frequencies, it tends to underestimate both the zero-point energy and the vibrational entropy while introducing artificial rigidity. Harmonic confining potentials eliminate imaginary frequencies and provide a flexible means to construct active-site models that can be used in unconstrained geometry relaxations, affording better convergence of reaction energies and barrier heights with respect to the model size, as compared to models with fixed-atom constraints.

13) Excited state rotational freedom impacts viscosity sensitivity in arylcyanoamide fluorescent molecular rotor dyes

RS Ehrlich, S Dasgupta, RE Jessup, KL Teppang, et.al. J. Phys. Chem. B 128, 3946 (2024) link

The microviscosity of intracellular environments plays an important role in monitoring cellular function. Thus, the capability of detecting changes in viscosity can be utilized for the detection of different disease states. Viscosity-sensitive fluorescent molecular rotors are potentially excellent probes for these applications; however, the predictable relationships between chemical structural features and viscosity sensitivity are poorly understood. Here, we investigate a set of arylcyanoamide-based fluorescent probes and the effect of small aliphatic substituents on their viscosity sensitivity. We found that the location of the substituents and the type of π-network of the fluorophore can significantly affect the viscosity sensitivity of these fluorophores. Computational analysis supported the notion that the excited state rotational energy barrier plays a dominant role in the relative viscosity sensitivity of these fluorophores. These findings provide valuable insight into the design of molecular rotor-based fluorophores for viscosity measurement.

12) Balance between physical interpretability and energetic predictability in widely used dispersion-corrected density functionals

S. Dasgupta*, E. Palos, Y.  Pan and F. Paesani*. J. Chem. Theory Comput. 20, 49 (2023) link

We assess the performance of different dispersion models for several popular density functionals across a diverse set of noncovalent systems, ranging from the benzene dimer to molecular crystals. By analyzing the interaction energies and their individual components, we demonstrate that there exists variability across different systems for empirical dispersion models, which are calibrated for reproducing the interaction energies of specific systems. Thus, parameter fitting may undermine the underlying physics, as dispersion models rely on error compensation among the different components of the interaction energy. Energy decomposition analyses reveal that, the accuracy of revPBE-D3 for some aqueous systems originates from significant compensation between dispersion and charge transfer energies. However, revPBE-D3 is less accurate in describing systems where error compensation is incomplete, such as the benzene dimer. Such cases highlight the propensity for unpredictable behavior in various dispersion-corrected density functionals across a wide range of molecular systems, akin to the behavior of force fields. On the other hand, we find that SCAN-rVV10, a targeted-dispersion approach, affords significant reductions in errors associated with the lattice energies of molecular crystals, while it has limited accuracy in reproducing structural properties. Given the ubiquitous nature of noncovalent interactions and the key role of density functional theory in computational sciences, the future development of dispersion models should prioritize the faithful description of the dispersion energy, a shift that promises greater accuracy in capturing the underlying physics across diverse molecular and extended systems.

11) Data-driven many-body potentials from density functional theory for aqueous phase chemistry

E. Palos, S. Dasgupta, E. Lambros and F. Paesani*. Chem. Phys. Rev. 4, 011301 (2023) link

Density functional theory (DFT) has been applied to modeling molecular interactions in water for over three decades. The ubiquity of water in chemical and biological processes demands a unified understanding of its physics, from the single molecule to the thermodynamic limit and everything in between. Recent advances in the development of data-driven and machine-learning potentials have accelerated simulation of water and aqueous systems with DFT accuracy. However, anomalous properties of water in the condensed phase, where a rigorous treatment of both local and non-local many-body (MB) interactions is in order, are often unsatisfactory or partially missing in DFT models of water. In this review, we discuss the modeling of water and aqueous systems based on DFT and provide a comprehensive description of a general theoretical/computational framework for the development of data-driven many-body potentials from DFT reference data. This framework, coined MB-DFT, readily enables efficient many-body molecular dynamics (MD) simulations of small molecules, in both gas and condensed phases, while preserving the accuracy of the underlying DFT model. Theoretical considerations are emphasized, including the role that the delocalization error plays in MB-DFT potentials of water and the possibility to elevate DFT and MB-DFT to near-chemical-accuracy through a density-corrected formalism. The development of the MB-DFT framework is described in detail, along with its application in MB-MD simulations and recent extension to the modeling of reactive processes in solution within a quantum mechanics/MB molecular mechanics (QM/MB-MM) scheme, using water as a prototypical solvent. Finally, we identify open challenges and discuss future directions for MB-DFT and QM/MB-MM simulations in condensed phases.

10) How good is the density-corrected SCAN functional for neutral and ionic aqueous systems, and what is so right about the Hartree-Fock density?

S. Dasgupta*, C. Shahi, P. Bhetwal, J.P. Perdew* and F. Paesani*. J. Chem. Theory Comput. 18, 4745 (2022) link

Density functional theory (DFT) is the most widely used electronic structure method, due to its simplicity and cost effectiveness. The accuracy of a DFT calculation depends not only on the choice of the density functional approximation (DFA) adopted but also on the electron density produced by the DFA. SCAN is a modern functional that satisfies all known constraints for meta-GGA functionals. The density-driven errors, defined as energy errors arising from errors of the self-consistent DFA electron density, can hinder SCAN from achieving chemical accuracy in some systems, including water. Density-corrected DFT (DC-DFT) can alleviate this shortcoming by adopting a more accurate electron density which, in most applications, is the electron density obtained at the Hartree–Fock level of theory due to its relatively low computational cost. In this work, we present extensive calculations aimed at determining the accuracy of the DC-SCAN functional for various aqueous systems. DC-SCAN (SCAN@HF) shows remarkable consistency in reproducing reference data obtained at the coupled cluster level of theory, with minimal loss of accuracy. Density-driven errors in the description of ionic aqueous clusters are thoroughly investigated. By comparison with the orbital-optimized CCD density in the water dimer, we find that the self-consistent SCAN density transfers a spurious fraction of an electron across the hydrogen bond to the hydrogen atom (H*, covalently bound to the donor oxygen atom) from the acceptor (OA) and donor (OD) oxygen atoms, while HF makes a much smaller spurious transfer in the opposite direction, consistent with DC-SCAN (SCAN@HF) reduction of SCAN overbinding due to delocalization error. While LDA seems to be the conventional extreme of density delocalization error, and HF the conventional extreme of (usually much smaller) density localization error, these two densities do not quite yield the conventional range of density-driven error in energy differences. Finally, comparisons of the DC-SCAN results with those obtained with the Fermi-Löwdin orbital self-interaction correction (FLOSIC) method show that DC-SCAN represents a more accurate approach to reducing density-driven errors in SCAN calculations of ionic aqueous clusters. While the HF density is superior to that of SCAN for noncompact water clusters, the opposite is true for the compact water molecule with exactly 10 electrons.

9) Density functional theory of water with the machine-learned DM21 functional

E. Palos†*, E. Lambros†*, S. Dasgupta†* and F. Paesani*. J. Chem. Phys. 156, 161103 (2022). link

The delicate interplay between functional-driven and density-driven errors in density functional theory (DFT) has hindered traditional density functional approximations (DFAs) from providing an accurate description of water for over 30 years. Recently, the deep-learned DeepMind 21 (DM21) functional has been shown to overcome the limitations of traditional DFAs as it is free of delocalization error. To determine if DM21 can enable a molecular-level description of the physical properties of aqueous systems within Kohn–Sham DFT, we assess the accuracy of the DM21 functional for neutral, protonated, and deprotonated water clusters. We find that the ability of DM21 to accurately predict the energetics of aqueous clusters varies significantly with cluster size. Additionally, we introduce the many-body MB-DM21 potential derived from DM21 data within the many-body expansion of the energy and use it in simulations of liquid water as a function of temperature at ambient pressure. We find that size-dependent functional-driven errors identified in the analysis of the energetics of small clusters calculated with the DM21 functional result in the MB-DM21 potential systematically overestimating the hydrogen-bond strength and, consequently, predicting a more ice-like local structure of water at room temperature.

8) Assessing the interplay between functional-driven and density-driven errors in DFT models of water

E. Palos*, E. Lambros*, S. Swee, J. Hu, S. Dasgupta and F. Paesani*. J. Chem. Theory Comput. 18, 3410 (2022). link

We investigate the interplay between functional-driven and density-driven errors in different density functional approximations within density functional theory (DFT) and the implications of these errors for simulations of water with DFT-based data-driven potentials. Specifically, we quantify density-driven errors in two widely used dispersion-corrected functionals derived within the generalized gradient approximation (GGA), namely BLYP-D3 and revPBE-D3, and two modern meta-GGA functionals, namely strongly constrained and appropriately normed (SCAN) and B97M-rV. The effects of functional-driven and density-driven errors on the interaction energies are first assessed for the water clusters of the BEGDB dataset. Further insights into the nature of functional-driven errors are gained from applying the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) to the interaction energies, which demonstrates that functional-driven errors are strongly correlated with the nature of the interactions. We discuss cases where density-corrected DFT (DC-DFT) models display higher accuracy than the original DFT models and cases where reducing the density-driven errors leads to larger deviations from the reference energies due to the presence of large functional-driven errors. Finally, molecular dynamics simulations are performed with data-driven many-body potentials derived from DFT and DC-DFT data to determine the effect that minimizing density-driven errors has on the description of liquid water. Besides rationalizing the performance of widely used DFT models of water, we believe that our findings unveil fundamental relations between the shortcomings of some common DFT approximations and the requirements for accurate descriptions of molecular interactions, which will aid the development of a consistent, DFT-based framework for the development of data-driven and machine-learned potentials for simulations of condensed-phase systems.

7) Elevating density functional theory to chemical accuracy for water simulations through a density-corrected many-body formalism

S. Dasgupta, E. Lambros, J.P. Perdew and F. Paesani*. Nat. Commun. 12, 6359 (2021). link

Density functional theory (DFT) has been extensively used to model the properties of water. Albeit maintaining a good balance between accuracy and efficiency, no density functional has so far achieved the degree of accuracy necessary to correctly predict the properties of water across the entire phase diagram. Here, we present density-corrected SCAN (DC-SCAN) calculations for water which, minimizing density-driven errors, elevate the accuracy of the SCAN functional to that of “gold standard” coupled-cluster theory. Building upon the accuracy of DC-SCAN within a many-body formalism, we introduce a data-driven many-body potential energy function, MB-SCAN(DC), that quantitatively reproduces coupled cluster reference values for interaction, binding, and individual many-body energies of water clusters. Importantly, molecular dynamics simulations carried out with MB-SCAN(DC) also reproduce the properties of liquid water, which thus demonstrates that MB-SCAN(DC) is effectively the first DFT-based model that correctly describes water from the gas to the liquid phase.

6) General many-body framework for data-driven potentials with arbitrary quantum mechanical accuracy: Water as a case study

E. Lambros†*, S. Dasgupta†*, E. Palos, S. Swee, J. Hu and F. Paesani*. J. Chem. Theory Comput. 17, 5635 (2021). link

We present a framework for developing data-driven many-body potential energy functions (MB-QM PEFs) representing interactions between small molecules at a quantum-mechanical (QM) level. We derive MB-QM PEFs for water from density functionals across different rungs of density functional theory (MB-DFT) and Møller–Plesset perturbation theory (MB-MP2). Analysis of MB contributions to water cluster interaction energies shows that all MB-QM PEFs match ab initio calculations, except for those derived from generalized gradient approximation (GGA) functionals. This discrepancy is attributed to density-driven errors in GGA functionals that inaccurately represent molecular interactions for different cluster sizes and hydrogen-bonding arrangements. We demonstrate that using density-corrected functionals (DC-DFT) within the MB formalism overcomes this limitation, resulting in a more accurate MB-DFT PEF derived from DC-PBE-D3 data that better reproduces ab initio results.

5) Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package

E. Epifanovsky et. al. J. Chem. Phys. 155, 084801 (2021). link

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced densitymatrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design.

4) Ab initio approach to femtosecond stimulated Raman spectroscopy: Investigating vibrational modes probed in excited-state relaxation of quaterthiophene.

S. Dasgupta and J. M. Herbert, J. Phys. Chem. A 124, 6356 (2020) link

We propose a protocol for simulating Femtosecond Stimulated Raman Spectroscopy (FSRS) by integrating ab initio molecular dynamics with computational resonance Raman spectroscopy. This allows us to monitor the time-dependent behavior of specific vibrational modes and gain insights into the underlying molecular motion responsible for the experimental FSRS signal. We apply this technique to study quaterthiophene derivatives and find that the relaxation of their S1 state involves in-phase and out-of-phase stretching modes, whose frequencies are linked to the dihedral backbone angle. The simulated spectra support the experimental assignment of vibrational modes probed in existing FSRS experiments on quaterthiophenes. This approach provides a valuable tool for investigating excited-state dynamics and confirming vibrational assignments in FSRS experiments.

3) Using atomic confining potentials for geometry optimizations and vibrational frequency calculations in quantum-chemical models of enzyme active sites.

S. Dasgupta and J. M. Herbert*, J. Phys. Chem. B 124, 1137 (2020) link

In quantum-chemical studies of enzymatic reaction mechanisms, simplified truncated active-site models are sometimes used as alternatives to mixed quantum mechanics molecular mechanics (QM/MM) procedures. However, introducing geometric constraints to prevent structural collapse of the model system during geometry optimizations can hinder efficiency and lead to artifacts like imaginary vibrational frequencies. We propose a simple alternative approach where terminal atoms of the model system are placed in soft harmonic confining potentials instead of rigid constraints. This modification is easy to implement and allows for unconstrained optimization while effectively fixing the anchor atoms in space. The new method is more efficient and robust for optimizing minima and transition states, avoiding unwanted imaginary frequencies. We demonstrate its effectiveness in enzymatic reaction pathways, accurately describing reaction paths and enabling calculation of vibrational zero-point and finite-temperature entropic corrections to barrier heights.

2) Ab initio investigation of the resonance Raman spectrum of the hydrated electron

S. Dasgupta, B. Rana and J. M. Herbert*, J. Phys. Chem. B 123, 8074 (2019) link

According to the conventional picture, the aqueous or “hydrated” electron, e(aq), occupies an excluded volume (cavity) in the structure of liquid water. However, simulations with certain one-electron models predict a more delocalized spin density for the unpaired electron, with no distinct cavity structure. It has been suggested that only the latter (non-cavity) structure can explain the hydrated electron’s resonance Raman spectrum, although this suggestion is based on calculations using empirical frequency maps developed for neat liquid water, not for e(aq). All-electron ab initio calculations presented here demonstrate that both cavity and non-cavity models of e(aq) afford significant red-shifts in the O–H stretching region. This effect is nonspecific and arises due to electron penetration into frontier orbitals of the water molecules. Only the conventional cavity model, however, reproduces the splitting of the H–O–D bend (in isotopically mixed water) that is observed experimentally and arises due to the asymmetric environments of the hydroxyl moieties in the electron’s first solvation shell. We conclude that the cavity model of e(aq) is more consistent with the measured resonance Raman spectrum than is the delocalized, non-cavity model, despite previous suggestions to the contrary. Furthermore, calculations with hybrid density functionals and with Hartree–Fock theory predict that non-cavity liquid geometries afford only unbound (continuum) states for an extra electron, whereas in reality this energy level should lie more than 3.0 eV below vacuum level. As such, the non-cavity model of e(aq) appears to be inconsistent with available vibrational spectroscopy, photoelectron spectroscopy, and quantum chemistry.

1) Standard grids for high-precision integration of modern density functionals: SG-2 and SG-3

S. Dasgupta and J. M. Herbert*, J. Comp. Chem.  38, 869 (2017) link

Density-functional approximations developed in the past decade necessitate the use of quadrature grids that are far more dense than those required to integrate older generations of functionals. This category of difficult-to-integrate functionals includes meta-generalized gradient approximations, which depend on orbital gradients and/or the Laplacian of the density, as well as functionals based on B97 and the popular “Minnesota” class of functionals, each of which contain complicated and/or oscillatory expressions for the exchange inhomogeneity factor. Following a strategy introduced previously by Gill and co-workers to develop the relatively sparse “SG-0” and “SG-1” standard quadrature grids, we introduce two higher-quality grids that we designate SG-2 and SG-3, obtained by systematically “pruning” medium- and high-quality atom-centered grids. The pruning procedure affords computational speedups approaching a factor of two for hybrid functionals applied to systems of  atoms, without significant loss of accuracy. The grid dependence of several popular density functionals is characterized for various properties.