## Publications

#### 74 Quantum Computation of Hydrogen Bond Dynamics and Vibrational Spectra

Philip Richerme, Melissa C. Revelle, Debadrita Saha, Sam A. Norrell, Christopher G. Yale, Daniel Lobser, Ashlyn D. Burch, Susan M. Clark, Jeremy M. Smith, Amr Sabry, and Srinivasan S. Iyengar. arXiv.

#### 73 Graph theoretic molecular fragmentation methods for electronic potential energy surfaces augmented by machine learning

Xiao Zhu, and Srinivasan S. Iyengar, arXiv.

#### 72 Graph-|Q⟩⟨C|, a Graph-Based Quantum/Classical Algorithm for Efficient Electronic Structure on Hybrid Quantum/Classical Hardware Systems: Improved Quantum Circuit Depth Performance

Juncheng Harry Zhang, and Srinivasan S. Iyengar, * J. Chem. Theory and Comput. * **Article ASAP**, 10.1021/acs.jctc.1c01303 (2022).
**Summary: ** Recently, multiple quantum computing technologies have emerged as potential alternative computational platforms to address complex computational challenges. Additionally, algorithms to
approximate electron correlation problems, for small molecular systems, and quantum nuclear dynamics problems have been implemented on quantum hardware devices. However, application of standard quantum circuit models to treat electronic structure problems leads to a rapid increase in the circuit depth and the number of quantum gates. This contributes greatly to the accumulated error during quantum propagation. This paper outlines a new hybrid quantum+classical algorithm based on a graph-theoretic approach to molecular fragmentation and is geared toward performing electron correlation calculations, potentially on an ensemble of quantum and classical hardware systems. The algorithm studied here is referred to as the “Graph-|Q⟩⟨C|” algorithm since it contains an independent set of classical and quantum algorithmic components inside a single umbrella. That is, the overall computational workload is partitioned, through graph theory based on computational complexity analysis, into (a) classical computing sections that are carried out on traditional classical electronic structure packages, and (b) quantum computing sections that are carried out using quantum circuit models. Furthermore, the Graph-|Q⟩⟨C| algorithm is quantum hardware-agnostic and is developed with the goal to be implemented on all quantum hardware technologies, and, in
fact, is designed to be used on an ensemble of such quantum hardware systems for any given calculation. In essence, our Graph-|Q⟩⟨C| algorithm yields a new approach that reduces the required quantum circuit depth, the number of quantum gates, and the number of CNOT gates (by several orders of magnitude) that contribute to error accumulation, through a graph-theory-based projection operator formalism. Thus, given this
reduction, our algorithm, potentially improves the quantum algorithmic efficiency, provides a new avenue for quantum resource management, and also reduces the accumulation of errors during the demonstrated electronic structure calculations on quantum hardware. Given the limitations of quantum circuit gate fidelities within the gate model, this algorithm, we expect, will become a central piece in the quantum/classical computing of chemical systems.

#### 71 Mapping quantum chemical dynamics problems to spin-lattice simulators

Debadrita Saha, Srinivasan S. Iyengar, Philip Richerme, Jeremy M. Smith, and Amr Sabry, * J. Chem. Theory and Comput. * **Articles ASAP.** (2021). DOI: https://doi.org/10.1021/acs.jctc.1c00688

**Summary: ** The accurate computational determination of chemical, materials, biological, and atmospheric properties has critical impact on a wide range of health and environmental problems, but is deeply limited by the computational scaling of quantum-mechanical methods. The complexity of quantum-chemical studies arises from the steep algebraic scaling of electron correlation methods, and the exponential scaling in studying nuclear dynamics and molecular flexibility. To date, efforts to apply quantum hardware to such quantum chemistry problems have focused primarily on electron correlation. Here, we provide a framework which allows for the solution of quantum chemical nuclear dynamics by mapping these to quantum spin-lattice simulators.

#### 70 Graph-theory based molecular fragmentation for efficient and accurate potential surface calculations in multiple dimensions

Anup Kumar, Nicole DeGregorio and Srinivasan S. Iyengar, * J. Chem. Theory and Comput. * **Articles ASAP.** (2021). DOI: https://doi.org/10.1021/acs.jctc.1c00065

** Summary: ** The accurate and efficient study of electronic structure and nuclear dynamics is at the core of multiple problems that are critical to materials, biological, and atmospheric research. However, these studies are deeply affected by the steep, polynomial scaling cost of electronic structure, and potentially exponential scaling of quantum nuclear dynamics. In this publication, we present a multi-topology molecular fragmentation approach, based on graph theory, to calculate multi-dimensional potential energy surfaces in agreement with post-Hartree-Fock levels of theory, but at DFT cost.

#### 69 Weighted-Graph-Theoretic Methods for Many-Body Corrections within ONIOM: Smooth AIMD and the Role of High-Order ManyBody Terms

Juncheng Harry Zhang, Timothy C. Ricard, Cody Haycraft, and Srinivasan S. Iyengar, * J. Chem. Theory and Comput. * **17**, 2672 (2021).

**Summary: ** We present a weighted-graph-theoretic approach to adaptively
compute contributions from many-body approximations for smooth and accurate
post-Hartree−Fock (pHF) ab initio molecular dynamics (AIMD) of highly fluxional
chemical systems

#### 68 An efficient and accurate approach to estimate hybrid functional and large basis set contributions to condensed phase systems and molecule-surface interactions

T. C. Ricard and S. S. Iyengar, * J. Chem. Theory and Comput. * **16**, 4790 (2020). (Supporting Information)

**Summary: ** We present an efficient approach to perform accurate hybrid DFT electronic structure calculations for condensed phase systems, at pure DFT cost.

#### 67 Embedded, graph-theoretically defined many-body approximations for wavefunction-in-DFT and DFT-in-DFT: applications to gas- and condensed-phase AIMD, and potential surfaces for quantum nuclear effects

Timothy C. Ricard, Anup Kumar and Srinivasan S. Iyengar, * Int. J. Quant. Chem. * In Press. (2020).

** Summary: ** We discuss a graph theoretic approach to adaptively compute many-body-approximations in an efficient manner to perform (a) accurate post-Hartree-Fock AIMD at DFT cost for medium to large sized molecular clusters, (b) hybrid DFT electronic structure calculations for condensed phase simulations at the cost of pure density functionals, (c) reduced cost on-the-fly basis extrapolation for gas-phase AIMD and condensed phase studies, and (d) similar basis-set extrapolations for condensed phase calculations, and (e) accurate post-Hartree-Fock level potential energy surfaces at DFT cost for quantum nuclear effects.

#### 66 Fragment-based electronic structure for potential energy surfaces using a superposition of fragmentation topologies

A. Kumar and S. S. Iyengar, "Fragment-based electronic structure for potential energy surfaces using a superposition of fragmentation topologies", * J. Chem. Theory and Comput. * **15**, 5769 (2019).

** Summary: ** Molecular fragmentation methods developed by us and by several groups have made it possible to perform accurate electronic structure calculations in large systems. However, problems exist with these ideas when are applied to molecular potential surface calculations where fragments may change as the nuclei move. We develop a Fragment-Based electronic structure method which adaptively utilizes multiple graphical representations for a given molecular system and use these to compute smooth potential energy surfaces in an efficent manner. Graph theory based representations are used to efficiently compute and represent the local interactions between coarse grain units of molecules leading to post-Hartree-Fock accurate results at DFT cost. Benchmarks are provided on protonated waterwire systems ubiquitous in numerous biological ion channels and in material applications.

#### 65 Challenges in constructing accurate methods for hydrogen transfer reactions in large biological assemblies: rare events sampling for mechanistic discovery and tensor networks for quantum nuclear effects

N. DeGregorio and S. S. Iyengar, "Challenges in constructing accurate methods for hydrogen transfer reactions in large biological assemblies: rare events sampling for mechanistic discovery and tensor networks for quantum nuclear effects", * Faraday Discussions * **221**, 379-405 (2019).

** Summary: ** The computational complexities arising in hydrogen transfer reactions within the active site of the enzymes is addressed through a new formalism of rare-events sampling for ab initio dynamics where wuantum nuclear effects are included through tensor networks. We begin with an ab initio molecular dynamics adaptation of the Caldeira–Leggett system bath Hamiltonian and the direct application of this method helps discover the active participation of isoleucine-839 in facilitating the hydrogen transfer in SLO-1. This was initially noted in * J. Phys. Chem. B. * **119**, 9532 (2015) and * J. Phys. Chem. B * ** 116 **, 10145 (2012) (see below). The rare event sampled reaction pathways are then complemented through quantum nuclear dynamics on potential energy surfaces along the biased molecular dynamics trajectories to obtain critical insights on quantum nuclear effects. Improved representation of quantum dynamics data, such as potential surfaces and wavepacket evolutions, is obtained using tensor networks.

#### 64 Adaptive Dimensional Decoupling for Compression of Quantum Nuclear Wave Functions and Efficient Potential Energy Surface Representations through Tensor Network Decomposition

N. DeGregorio and S. S. Iyengar, "Adaptive Dimensional Decoupling for Compression of Quantum Nuclear Wave Functions and Efficient Potential Energy Surface Representations through Tensor Network Decomposition", * J. Chem. Theory and Comput. * **15**, 2780 (2019).

** Summary: ** An approach to reduce the computational complexity and storage pertaining to quantum nuclear wave functions and potential energy surfaces is discussed. The method utilizes tensor networks; two specific forms of tensor networks are considered. (a) The well-known matrix product state is evaluated. (b) The wave function and potential energy surface space is initially partitioned into “system” and “bath” degrees of freedom, following which the individual system and bath tensors are in turn decomposed as matrix product states. Using these methods drastically reduces the overall storage and computational cost.

#### 63 Photoelectrons are not always quite free

Jarrett L. Mason, Josey E. Topolski, Joshua Ewigleben, Srinivasan S. Iyengar, and Caroline Chick Jarrold, "Photoelectrons are not always quite free", * J. Phys. Chem. Lett.* **10**, 144 (2019).

#### 62 Efficiently capturing weak interactions in ab initio molecular dynamics with on the fly basis set extrapolation

T. C. Ricard and S. S. Iyengar, "Efficiently capturing weak interactions in *ab initio* molecular dynamics with on the fly basis set extrapolation", * J. Chem. Theory and Comput. * **14**, 5535 (2018).

#### 61 Exotic electronic structures in Sm_{x}Ce_{3-x}O_{y} (x=0-3; y=2-4) clusters, and the effect of high neutral density of low-lying states on photodetachment transition intensities

J. E. Topolski, J. O. Kafader, V. Marrero-Colon, S. S. Iyengar H. P. Hratchian and C. C. Jarrold, "Exotic electronic structures in Sm_{x}Ce_{3-x}O_{y} (x=0-3; y=2-4) clusters, and the effect of high neutral density of low-lying states on photodetachment transition intensities", * J. Chem. Phys.* **149**, 054305 (2018).

#### 60 Adaptive, geometric networks for efficient coarse-grained ab initio molecular dynamics with post-Hartree-Fock accuracy

T. C. Ricard, C. Haycraft, and S. S. Iyengar, "Adaptive, geometric networks for efficient coarse-grained ab initio molecular dynamics with post-Hartree-Fock accuracy", * J. Chem. Theory and Comput. * **14**, 30 (2018).

#### 59 Efficient and adaptive methods for computing accurate potential surfaces for quantum nuclear effects: Applications to hydrogen transfer reactions

N. DeGregorio and S. S. Iyengar, "Efficient and adaptive methods for computing accurate potential surfaces for quantum nuclear effects: Applications to hydrogen transfer reactions" * J. Chem. Theory and Comput. * **14**, 30 (2018).

** Summary: ** The exponentially scaling multi-dimensional nuclear potential energy surface space is tesselated using (a) Shannon information entropy, and (b) a sampling function determiend by the potential energy, its nuclear gradients and wavepacket density. The methods are used to efficiently compute potential surfaces for hydrogen transfer problems of interest in atmospheric and biological problems.

#### 58 Proton relays in anomalous carbocations dictate spectroscopy, stability and mechanisms: Case studies on C_{2}H_{5}^{+} and C_{3}H_{3}^{+}

L. M. Sager and S. S. Iyengar, "Proton relays in anomalous carbocations dictate spectroscopy, stability and mechanisms: Case studies on C_{2}H_{5}^{+} and C_{3}H_{3}^{+}" * Phys. Chem. Chem. Phys. * **19**, 27801 (2017).

#### 57 The electron shuttle: Cerium influences samaraium 4f orbital occupancy in heteronuclear Ce-Sm oxide clusters

J. O. Kafader, J. E. Topolski, V. Marrero-Colon, S. S. Iyengar and C. C. Jarrold, "The electron shuttle: Cerium influences samaraium 4f orbital occupancy in heteronuclear Ce-Sm oxide clusters". * J. Chem. Phys.* **146**, 194310 (2017).

#### 56 Efficient, 'On-the-fly', Born-Oppenheimer and Car-Parrinello-type dynamics with coupled cluster (CCSD) accuracy through fragment based electronic structure

C. Haycraft, J. Li and S. S. Iyengar, "Efficient, 'On-the-fly', Born-Oppenheimer and Car-Parrinello-type dynamics with coupled cluster (CCSD) accuracy through fragment based electronic structure" * J. Chem. Theory and Comput. * **13**, 1885 (2017). Supporting Information: Click here

#### 55 A Grotthuss-like proton shuttle in the anomalous C_{2}H_{3}^{+} Carbocation: Energetic and vibrational properties for isotopologues

J. Li, A. B. Pacheco, K. Raghavachari and S. S. Iyengar, "A Grotthuss-like proton shuttle in the anomalous C_{2}H_{3}^{+} Carbocation: Energetic and vibrational properties for isotopologues" * Phys. Chem. Chem. Phys. * **18**, 29395 (2016). (Click here for supporting information.)

#### 54 Hybrid extended Lagrangian, post-Hartree-Fock Born-Oppenheimer ab initio molecular dynamics with fragment-based electronic structure

J. Li, C. Haycraft and S. S. Iyengar "Hybrid extended Lagrangian, post-Hartree-Fock Born-Oppenheimer ab initio molecular dynamics with fragment-based electronic structure". * J. Chem. Theory and Comput. * **12**, 2493 (2016).

#### 53 Ab initio molecular dynamics using recursive, spatially separated, overlapping model subsystems mixed within an ONIOM based fragmentation energy extrapolation technique

J. Li and S. S. Iyengar "Ab initio molecular dynamics using recursive, spatially separated, overlapping model subsystems mixed within an ONIOM based fragmentation energy extrapolation technique". * J. Chem. Theory and Comput. * **11**, 3978 (2015).

#### 52 Active site dynamical effects that affect the hydrogen transfer rate-limiting step in the catalysis of linoleic acid by soybean lipoxygenase-1 (SLO-1): Primary and Secondary Isotope effects

P. Phatak, J. Vanderley, J. deBrota, J. Li and S. S. Iyengar, "Active site dynamical effects that affect the hydrogen transfer rate-limiting step in the catalysis of linoleic acid by soybean lipoxygenase-1 (SLO-1): Primary and Secondary Isotope effects". * J. Phys. Chem. B. * **119**, 9532 (2015).

#### 51 A multi-wavelet treatment of the quantum subsystem in quantum wavepacket ab-initio molecular dynamics through an hierarchical partitioning of momentum space

A. H. Prociuk and S. S. Iyengar, "A multi-wavelet treatment of the quantum subsystem in quantum wavepacket ab-initio molecular dynamics through an hierarchical partitioning of momentum space", * J. Chem. Theory Comput. * **10**, 2950 (2014).

#### 50 Multi-configurational generalizations to the "on-the'fly" electronic structure calculations within quantum wavepacket ab initio molecular dynamics (QWAIMD): Applications to the study of vibrational properties in hydrogen bonded systems

J. Li, X. Li and S. S. Iyengar, "Multi-configurational generalizations to the "on-the'fly" electronic structure calculations within quantum wavepacket ab initio molecular dynamics (QWAIMD): Applications to the study of vibrational properties in hydrogen bonded systems", * J. Chem. Theory Comput. * **10**, 2265 (2014).

#### 49 Teaching Thermodynamics and Kinetics to Advanced General Chemistry Students and to Upper-Level Undergraduate Students Using PV Diagrams

S. S. Iyengar and R. T. deSouza, "Teaching Thermodynamics and Kinetics to Advanced General Chemistry Students and to Upper-Level Undergraduate Students Using PV Diagrams", * J. Chem. Ed. * **91**, 74 (2014).

#### 48 Using Quantum Mechanics To Facilitate the Introduction of a Broad Range of Chemical Concepts to First-Year Undergraduate Students

R. T. deSouza and S. S. Iyengar, "Using Quantum Mechanics To Facilitate the Introduction of a Broad Range of Chemical Concepts to First-Year Undergraduate Students", * J. Chem. Ed. * **90**, 717 (2013).

#### 47 Constructing periodic phase space orbits from ab initio molecular dynamics trajectories to analyze vibrational spectra: case study of the Zundel (H5O2+) cation

S. M. Dietrick and S. S. Iyengar, "Constructing periodic phase space orbits from ab initio molecular dynamics trajectories to analyze vibrational spectra: case study of the Zundel (H5O2+) cation", In Press. * J. Chem. Theory and Comp. * ** 8 **, 4876 (2012).

#### 46 Gauging the flexibility of the active site in soybean lipoxygenase-1 (SLO-1) through an atom-centered density matrix propagation (ADMP) treatment that facilitates the sampling of rare events

P. Phatak, I. Sumner and S. S. Iyengar, "Gauging the flexibility of the active site in soybean lipoxygenase-1 (SLO-1) through an atom-centered density matrix propagation (ADMP) treatment that facilitates the sampling of rare events", * J. Phys. Chem. B * ** 116 **, 10145 (2012).

#### 45 'Pump-probe' atom-centered density matrix propagation studies to gauge anharmonicity and energy repartitioning in atmospheric reactive adducts: Case study of the OH + Isoprene and OH + Butadiene reaction intermediates

A. B. Pacheco, S. M. Dietrick, P. S. Stevens and S. S. Iyengar, "'Pump-probe' atom-centered density matrix propagation studies to gauge anharmonicity and energy repartitioning in atmospheric reactive adducts: Case study of the OH + Isoprene and OH + Butadiene reaction intermediates", * J. Phys. Chem. A * ** 116 **, 4108 (2012).

#### 44 The influence of water on anharmonicity, stability and vibrational energy distribution of hydrogen-bonded adducts in atmospheric reactions: Case study of Hydroxy Isoprene using ab-initio Molecular Dynamics

S. M. Dietrick, A. B. Pacheco, P. Phatak, P. S. Stevens and S. S. Iyengar, "The influence of water on anharmonicity, stability and vibrational energy distribution of hydrogen-bonded adducts in atmospheric reactions: Case study of Hydroxy Isoprene using ab-initio Molecular Dynamics", * J. Phys. Chem. A * ** 116 **, 399 (2012).

#### 43 Quantum Wave-packet Ab Initio Molecular dynamics for extended systems

X. Li and S. S. Iyengar, "Quantum Wave-packet Ab Initio Molecular dynamics for extended systems" * J. Phys. Chem. A * ** 115 **, 6269 (2011).

#### 42 Multi-Stage Ab-initio Quantum Wavepacket Dynamics for Electronic Structure and Dynamics in open systems: Momentum Representation, Coupled Electron Nuclear dynamics and External Fields

A. B. Pacheco and S. S. Iyengar, "Multi-Stage Ab-initio Quantum Wavepacket Dynamics for Electronic Structure and Dynamics in open systems: Momentum Representation, Coupled Electron Nuclear dynamics and External Fields" * J. Chem. Phys.* ** 134 **, 074107 (2011).

#### 41 Shannon information entropy based time-dependent deterministic sampling techniques for efficient on-the-fly quantum dynamics and electronic structure

D. Hocker, X. Li and S. S. Iyengar, "Shannon information entropy based time-dependent deterministic sampling techniques for efficient on-the-fly quantum dynamics and electronic structure" * J. Chem. Theory and Comp. * **7**, 256 (2011).

#### 40 Quantum wavepacket ab initio molecular dynamics: Generalizations using an extended Lagrangian treatment of diabatic states coupled through multi-reference electronic structure

X. Li and S. S. Iyengar, "Quantum wavepacket *ab initio* molecular dynamics: Generalizations using an extended Lagrangian treatment of diabatic states coupled through multi-reference electronic structure" * J. Chem. Phys.* **133**, 184105 (2010).

#### 39 A Multi-Stage Ab-initio Quantum Wavepacket Dynamics Formalism for Electronic Structure and Dynamics in Open Systems

A. B. Pacheco and S. S. Iyengar, "A Multi-Stage Ab-initio Quantum Wavepacket Dynamics Formalism for Electronic Structure and Dynamics in Open Systems" * J. Chem. Phys. * **133**, 044105 (2010).

#### 38 Isotope dependent, temperature regulated, energy repartitioning in a low-barrier, short-strong hydrogen bonded cluster

X. Li, J. Oomens, J. R. Eyler, D. T. Moore, S. S. Iyengar, "Isotope dependent, temperature regulated, energy repartitioning in a low-barrier, short-strong hydrogen bonded cluster" * J. Chem. Phys. * **132**, 244301 (2010).

#### 37 Analysis of Hydrogen Tunneling in an Enzyme Active Site Using von Neumann Measurements

I. Sumner and S. S. Iyengar, "Analysis of Hydrogen Tunneling in an Enzyme Active Site Using von Neumann Measurements" * Journal of Chemical Theory and Computation * ** 6 **, 1698 (2010).

#### 36 Computing vibrational properties in hydrogen bonded systems using Quantum wavepacket ab initio molecular dynamics

S. S. Iyengar, "Computing vibrational properties in hydrogen bonded systems using Quantum wavepacket ab initio molecular dynamics" * Int. J. Quant. Chem. * ** 109 **, 3798 (2009).

#### 35 Combining quantum wavepacket ab initio molecular dynamics (QWAIMD) with QM/MM and QM/QM techniques: Implementation blending ONIOM and empirical valence bond theory

I. Sumner and S. S. Iyengar, "Combining quantum wavepacket ab initio molecular dynamics (QWAIMD) with QM/MM and QM/QM techniques: Implementation blending ONIOM and empirical valence bond theory" * J. Chem. Phys. * ** 129**, 054109 (2008).

#### 34 Experimental and theoretical study of the kinetics of the OH + 1,3-butadiene reaction between 263 and 423 K at low pressure

D. Vimal, A. B. Pacheco, S. S. Iyengar and P. S. Stevens, "Experimental and theoretical study of the kinetics of the OH + 1,3-butadiene reaction between 263 and 423 K at low pressure". * J. Phys. Chem. A* ** 112**, 7227 (2008).

#### 33 Hydrogen tunneling in an enzyme active site: a quantum wavepacket dynamical perspective

S. S. Iyengar, I. Sumner and J. Jakowski "Hydrogen tunneling in an enzyme active site: a quantum wavepacket dynamical perspective". * J. Phys. Chem. B * ** 112**, 7601 (2008).

#### 32 Insights from first principles molecular dynamics studies towards infra-red multiple-photon and single-photon action spectroscopy: Case study of the proton-bound di-methyl ether dimer

X. Li, D. T. Moore and S. S. Iyengar, "Insights from first principles molecular dynamics studies towards infra-red multiple-photon and single-photon action spectroscopy: Case study of the proton-bound di-methyl ether dimer". * J. Chem. Phys. * ** 128 **, 184308 (2008).

#### 31 The study of dynamically averaged vibrational spectroscopy of atmospherically relevant clusters using ab initio molecular dynamics in conjunction with quantum wavepackets

S. S. Iyengar, X. Li and I. Sumner "The study of dynamically averaged vibrational spectroscopy of atmospherically relevant clusters using ab initio molecular dynamics in conjunction with quantum wavepackets". * Adv. Quant. Chem. * ** 55 **, 333 (2008).

#### 30 Multiscale Theory of Collective and Quasi-Particle Modes in Quantum Nanosystems

P. Ortoleva and S. S. Iyengar, "Multiscale Theory of Collective and Quasi-Particle Modes in Quantum Nanosystems". * J. Chem. Phys* ** 128 **, 164716 (2008)

#### 29 Quantum Wavepacket Ab Initio Molecular Dynamics: An approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects

I. Sumner and S. S. Iyengar "Quantum Wavepacket Ab Initio Molecular Dynamics: An approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects". * J. Phys. Chem. A*, ** 111 **, 10313-10324 (2007).

#### 28 Further analysis of the dynamically averaged vibrational spectrum for the 'magic' protonated 21-water cluster

S. S. Iyengar "Further analysis of the dynamically averaged vibrational spectrum for the 'magic' protonated 21-water cluster". * J. Chem. Phys. * ** 126 **, 216101 (2007).

#### 27 Can the four-coordinated, penta-valent oxygen in hydroxide water clusters be detected through experimental vibrational spectroscopy?

X. Li, V. E. Teige and S. S. Iyengar "Can the four-coordinated, penta-valent oxygen in hydroxide water clusters be detected through experimental vibrational spectroscopy?". * J. Phys. Chem. A * ** 111 **, 4815-4820 (2007).

#### 26 Computational Improvements to Quantum Wavepacket Ab Initio Molecular Dynamics using a potential-adapted, time-dependent deterministic sampling technique

J. Jakowski, I. Sumner and S. S. Iyengar, "Computational Improvements to Quantum Wavepacket Ab Initio Molecular Dynamics using a potential-adapted, time-dependent deterministic sampling technique". * Journal of Chemical Theory and Computation* ** 2 ** 1203-1219 (2006).

#### 25 Ab Initio Dynamics with wave-packets and density matrices

S. S. Iyengar, "Ab Initio Dynamics with wave-packets and density matrices". * Theo. Chem. Accts.* ** Special issue on "New Perspectives in Theoretical Chemistry" ** Vol. 116, 326-337 (2006)

#### 24 The Properties of Ion-Water Clusters. II. Solvation structures of Na+, Cl- and H+ clusters as a function of temperature

C. J. Burnham, M. K. Petersen, T. J. F. Day, S. S. Iyengar and G. A. Voth, "The Properties of Ion-Water Clusters. II. Solvation structures of Na+, Cl- and H+ clusters as a function of temperature". * J. Chem. Phys. * ** 124 **, 024327 (2006)

#### 23 Quantum Wavepacket Ab Initio Molecular Dynamics: An approach to study quantum dynamics in large systems

S. S. Iyengar and J. Jakowski, "Quantum Wavepacket Ab Initio Molecular Dynamics: An approach to study quantum dynamics in large systems". * J. Chem. Phys.* ** 122 ** 114105-114115 (2005).

#### 22 Dynamical effects on vibrational and electronic spectra of HO2 water clusters: an ab initio molecular dynamics study

S. S. Iyengar, "Dynamical effects on vibrational and electronic spectra of HO_{2} water clusters: an ab initio molecular dynamics study". * J. Chem. Phys. * ** 123 **, 084310 (2005)

#### 21 The Properties of Ion-Water Clusters. I. The Protonated 21-Water Cluster

S. S. Iyengar, M. K. Petersen, C. J. Burnham, T. J. F. Day, V. E. Teige and G. A. Voth, "The Properties of Ion-Water Clusters. I. The Protonated 21-Water Cluster". * J. Chem. Phys. * ** 123 **, 084309 (2005)

#### 20 On the Amphiphilic Behavior of the Hydrated Proton: An Ab Initio Molecular Dynamics Study

S. S. Iyengar, T. J. F. Day, and G. A. Voth, "On the Amphiphilic Behavior of the Hydrated Proton: An Ab Initio Molecular Dynamics Study". * Int. J. Mass Spectrometry * ** 241**, 197-204 (2005).

#### 19 Comment on ``Curvy-steps approach to constraint-free extended-Lagrangian ab initio molecular dynamics, using atom-centered basis functions: Convergence toward Born-Oppenheimer trajectories

S. S. Iyengar, H. B. Schlegel, G. E. Scuseria, J. M. Millam and M. J. Frisch, "Comment on ``Curvy-steps approach to constraint-free extended-Lagrangian ab initio molecular dynamics, using atom-centered basis functions: Convergence toward Born-Oppenheimer trajectories''[J. Chem. Phys. **121**, 11542 (2004)]". * J. Chem. Phys.*** 123 **, 027101 (2005)

#### 18 The Hydrated Proton at the Water Liquid/Vapor Interface

M. K. Petersen, S. S. Iyengar, C. J. Burnham, T. J. F. Day, and G. A. Voth, "The Hydrated Proton at the Water Liquid/Vapor Interface". * J. Phys. Chem. B* ** 108 **, 14804 (2004).

#### 17 Effect of time-dependent basis functions and their superposition error on Atom-centered Density Matrix Propagation (ADMP): Connections to Wavelet theory of multi-resolution analysis

S. S. Iyengar and M. J. Frisch, "Effect of time-dependent basis functions and their superposition error on Atom-centered Density Matrix Propagation (ADMP): Connections to Wavelet theory of multi-resolution analysis". * J. Chem. Phys.***121**, 5061 (2004)

#### 16 Hybrid Ab-Initio/Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-centered Density Matrix Propagation (ADMP) Approach

N. Rega, S. S. Iyengar, G. A. Voth, H. B. Schlegel, T. Vreven and M. J. Frisch, "Hybrid Ab-Initio/Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-centered Density Matrix Propagation (ADMP) Approach". * J. Phys. Chem. B * **108** 4210-4220 (2004).

#### 15 Modeling Condensed-phase chemistry through molecular dynamics simulation

S. S. Iyengar, C. J. Burnham, M. K. Petersen, and G. A. Voth, "Modeling Condensed-phase chemistry through molecular dynamics simulation", *Computers in Science and Engineering * ** 5 ** Iss. 3, 31-35 (2003). (special issue on Computational Chemistry)

#### 14 Atom-centered Density Matrix Propagation: Generalizations using Bohmian mechanics

S. S. Iyengar, H. B. Schlegel, and G. A. Voth, "Atom-centered Density Matrix Propagation: Generalizations using Bohmian mechanics", * J. Phys. Chem. A. * ** 107 ** 7269-7277 (2003). (Festschrift in honor of Professor Donald J. Kouri)

#### 13 Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian orbitals. IV. Formal Analysis of the deviations from Born-Oppenheimer dynamics

S. S. Iyengar, H. B. Schlegel, G. A. Voth, J. M. Millam, G. E. Scuseria, M. J. Frisch, "Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian orbitals. IV. Formal Analysis of the deviations from Born-Oppenheimer dynamics". *Israel J. Chem* ** 7 ** 191, 2002. (Special Issue on Condensed Phase Dynamics)

#### 12 Quantum reactive scattering in three dimensions using hyperspherical (APH) coordinates: Periodic Distributed Approximating Functionals (PDAF) method for surface functions

K. Zhang, G. A. Parker, D. J. Kouri, D. K. Hoffman, S. S. Iyengar, "Quantum reactive scattering in three dimensions using hyperspherical (APH) coordinates: Periodic Distributed Approximating Functionals (PDAF) method for surface functions". *J. Chem. Phys.***118**, 569 (2003).

#### 11 Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian orbitals. III. Comparison with Born-Oppenheimer Dynamics

H. B. Schlegel, S. S. Iyengar, X. Li, J. M. Millam, G. A. Voth, G. E. Scuseria, M. J. Frisch, "Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian orbitals. III. Comparison with Born-Oppenheimer Dynamics".*J. Chem. Phys. ***117**, 8694 (2002).

#### 10 Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian orbitals. II. Generalizations based on Mass-weighting, Idempotency, Energy Conservation and Choice of Initial Conditions

S. S. Iyengar, H. B. Schlegel, J. M. Millam, G. A. Voth, G. E. Scuseria, M. J. Frisch, "Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian orbitals. II. Generalizations based on Mass-weighting, Idempotency, Energy Conservation and Choice of Initial Conditions" *J. Chem. Phys.* **115**, 10291 (2001).

#### 9 The Challenge of Creating Accurate and Effective Kinetic Energy Functionals

S. S. Iyengar, M. Ernzerhoff, S.N. Maximoff, G. E. Scuseria, "The Challenge of Creating Accurate and Effective Kinetic Energy Functionals". *Phys. Rev. A ***63** (2001) 052508

#### 8 Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals

H. B. Schlegel, J. M. Millam, S. S. Iyengar, G. A. Voth, A. D. Daniels, G. E. Scuseria, M. J. Frisch, "Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals". *J. Chem. Phys. * **114***, 9758* (2001).

#### 7 Particular and Homogeneous Solutions of Time-Independent Wavepacket Schrodinger Equations: Calculations Using a Subset of Eigenstates of Undamped or Damped Hamiltonians

S. S. Iyengar, D. J. Kouri, D. K. Hoffman, "Particular and Homogeneous Solutions of Time-Independent Wavepacket Schrodinger Equations: Calculations Using a Subset of Eigenstates of Undamped or Damped Hamiltonians". *Theoretical Chemistry Accounts.* **104** (2000) 471-483.

#### 6 Bounding the Extrapolated Correlation Energy Using Pade Approximants

S. S. Iyengar, G. E. Scuseria, A. Savin, "Bounding the Extrapolated Correlation Energy Using Pade Approximants". *Int. J. Quant. Chem.* **79** (2000) 222-234

#### 5 Estimating the Upper and Lower Bounds for the Eigenvalues of any matrix

S. S. Iyengar, D. J. Kouri, G. A. Parker, D. K. Hoffman, "Estimating the Upper and Lower Bounds for the Eigenvalues of any matrix". *Theoretical Chemistry Accounts. ***103** (2000) 507-517.

#### 4 Symmetry-Adapted Distributed Approximating Functionals: Theory and application to the ro-vibrational states of H_{3}^{+}

S. S. Iyengar, G. A. Parker, D. J. Kouri, D. K. Hoffman, "Symmetry-Adapted Distributed Approximating Functionals: Theory and application to the ro-vibrational states of H_{3}^{+}". *J. Chem. Phys. ***110**, 10283 (1999).

#### 3 Further Analysis of Solutions to the Time-Independent Wavepacket Equations of Quantum Dynamics II: Scattering as a Continuous Function of Energy Using Finite, Discrete Approximate Hamiltonians

Y. Huang, S. S. Iyengar, D. J. Kouri, D. K. Hoffman, "Further Analysis of Solutions to the Time-Independent Wavepacket Equations of Quantum Dynamics II: Scattering as a Continuous Function of Energy Using Finite, Discrete Approximate Hamiltonians" *J. Chem. Phys.* **105**, 927 (1996).

#### 2 Inclusion of molecular flexibility in Partition Coefficient calculations on oligopeptides using stochastic sampling

N. G. J. Richards, P. B. Williams, S. S. Iyengar, *Proceedings of the twenty-seventh Hawaii International Conference on System Sciences* 203 (1994).

#### 1 Semi-empirical calculations on the mechanism of enniatin B mediated transport of sodium ions

S. N. Datta, S. S. Iyengar, "Semi-empirical calculations on the mechanism of enniatin B mediated transport of sodium ions" *Chem. Phys. Lett.* ** 183**, 491 (1991).