Computing Quantum Chemical Results without Doing
Quantum Chemistry: A Machine Learning Shortcut
Mojtaba Haghighatlari1, Johannes Hachmann
1,2,3
1Department of Chemical and Biological Engineering,
2Computational and Data-Enabled Science and Engineering Graduate Program,
University at Buffalo, SUNY, Buffalo, New York 14260, USA
3New York State Center of Excellence in Materials Informatics,
Buffalo, New York 14203, USA
ABSTRACT
Computational quantum chemistry is a valuable tool that allows us to characterize and assess
compounds, materials, and reactions. It is based on the notion that quantum mechanics
rigorously maps a given chemical structure to its properties. Unfortunately, this mapping is
expensive and does not lend itself to generalizations that correspond to chemical intuition,
empirical rules, and well-known trends. Our work addresses the question if machine learning
– given a suitable training set – can recover this mapping in simplified form, which would
offer a shortcut to quantum chemical results without the need to perform quantum chemical
calculations. Such a shortcut would open the door to rapid high-throughput screening
capabilities, which would enable an unprecedented exploration of chemical space.
We will present our latest chemical data mining approaches that allow us to extract an
understanding of hidden structure-property relationships in large-scale data sets and to
quantify these in model equations. We will discuss the utility of these innovative machine
learning, statistical learning, and informatics techniques as well as the error bars and
predictive performance of the resulting models. In this context, we will introduce CheML,
our machine learning and informatics software suite for the chemical and materials sciences.
Oral presentation preferred.
Coupled-Cluster Interpretation of the Photoelectron Spectra of Ag3-
and Au3-
Nicholas P. Bauman,1 Jared A. Hansen,1 Piotr Piecuch,1,2 and Masahiro Ehara3,4
1Department of Chemistry, Michigan State University, East Lansing, MI 48824, U.S.A.
2Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, U.S.A.
3Institute for Molecular Science and Research Center for Computational Science, Okazaki 444-8585, Japan
4Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto 615-8245, Japan
We undertake a thorough ab initio study of the photoelectron spectra of silver and gold trimer anions,1,2 Ag3
- and Au3-, by examining the ground and excited states of the corresponding neutral
particles, Ag3 and Au3, employing the scalar relativistic ionized equation-of-motion coupled-cluster (IP-EOMCC) approximations. We examine the effects of basis set, number of correlated electrons, level of applied theory including up to 3-hole-2-particle terms, and geometry relaxation. The IP-EOMCC methods allow one to obtain the ground and excited states of the
(N − 1)-electron open-shell system by applying the linear ionizing operator, ��岫�−1岻, to the ground state of the corresponding N-electron closed-shell core obtained with a single-reference CC approach. In this way, one can properly account for spin symmetry that the conventional, particle-conserving, open-shell CC/EOMCC approaches have difficulties with, while determining the electronic spectrum of the (N − 1)-electron system obtained by removing an electron from the N-electron closed-shell species. To further improve the accuracy, we adopt a simple IP-EOMCC-based extrapolation scheme that captures the important higher-order many-electron correlation contributions to the energy in an approximate, but computationally efficient manner, in addition to the basis set effects and the correlation effects associated with semi-core electrons. Our IP-EOMCC calculations provide an accurate and complete assignment of peaks and shoulders in the experimental photoelectron spectra of Ag3
- and Au3- for the first time.
1 H. Handschuh, C.-Y. Cha, P.S. Bechthold, G. Ganteför, and W. Eberhardt, J. Chem. Phys. 102, 6406 (1995). 2 H. Handschuh, G. Ganteför, P.S. Bechthold, and W. Eberhardt, J. Chem. Phys. 100, 7093 (1994). 3 N.P. Bauman, J.A. Hansen, M. Ehara, and P. Piecuch, J. Chem. Phys. 141, 101102 (2014). 4 N.P. Bauman, J.A. Hansen, and P. Piecuch, in preperation.
Structure of the One-particle reduced densitymatrix from Generalized Pauli exclusion
principle
Romit Chakraborty and David A. Mazziotti
June 19, 2015
The Pauli exclusion principle requires that the occupations of the orbitals lie be-tween zero and one. These Pauli conditions hold for one-electron reduced densitymatrices (1-RDMs) from both open and closed quantum systems. More than 40 yearsago, it was recognized that there are additional conditions on the 1-RDM for closedquantum systems. In this review we discuss the structure of the 1-RDM from thegeneralized Pauli exclusion principle in many-electron atoms and molecules and theviolation of the generalized Pauli principle as a sufficient condition for the opennessof a many-electron quantum system.
**I would like to give a contributed talk**
1
Molecular Dynamic simulations of CO-induced surface reconstruction
and island formation on Pt, Pd, and Pt/Pd (557) surfaces Joseph R. Michalka and J. Daniel Gezelter
1
University of Notre Dame 1251 Nieuwland Science Hall, Notre Dame, Indiana, 46556, United States,
(574)-631-7595, [email protected]
Platinum and Palladium surfaces and nanoparticles are of prime importance in many
catalytic processes. The catalytic activity of these species is strongly influenced by their
displayed facets and availability of under-coordinated metal binding sites. The presence
of adsorbates, here carbon monoxide (CO), can lead to significant surface restructuring.
Using molecular dynamics simulations, we model CO-induced surface restructuring on
high-index Pt, Pd, and Pt/Pd surfaces. Whereas CO adsorbed to Pt (557) leads to
increased surface mobility of Pt and a doubling of the step-edges, CO on Pd (557)
maintains the high-index facet. CO on a Pd (557) system covered with one layer of Pt
leads to domains of Pt and an exposure of the underlying Pd. Metallic self and cross
interactions are described using the Embedded Atom Method, while metal-CO
interactions were parameterized from experimental data and theoretical (DFT)
calculations.
If a slot is available, I wish to give a talk.
The Molecular Origin of Color tuning of Deep‐water Lake Baikal Cottoid Fish
Visual Pigments
Hoi Ling Luk1, Fabio Montisci2, Federico Melaccio2, Nihar Bhattacharyya3, James
Morrow3, Belinda S. W. Chang3, Francesca Fanelli4, Massimo Olivucci1,2
1Department of Chemistry, Bowling Green State University, Bowling Green OH 43403 2Università di Siena, Dipartimento di Chimica, via A. De Gasperi 2, I‐53100, Siena, Italy 3Department of Ecology and Evolutionary Biology and Department of Cell and Systems
Biology, University of Toronto, 25 Harbord St., Toronto, ON M5S 3G5, Canada. 4Dulbecco Telethon Institute, Department of Life Sciences, University of Modena and
Reggio Emilia, I‐41125 Modena, Italy
Lake Baikal is located in Eastern Siberia and is the deepest and most ancient lakes in
the world. Its deepness provides the colonization of all depth habitats by a unique
fauna that includes a remarkable flock of largely endemic teleost fish of the sub‐
order Cottoidei. These cottoid fishes shows a gradual blueshift in the absorption
maxima (λmax) of their visual pigments in relation to the depth of their habitat and
such spectral shifts do not arise from alternative chromophores as all visual
pigments in the Baikal cottoid fishes contain 11‐cis‐retinal chromophore. Hence, this
differing λmax could have arisen by single amino acid substitutions from an ancestor
which phylogenetics study indicates that the ancestral species to the Baikal flock
had a rod pigment with a λmax around 505 nm. In order to understand the origin of
such color tuning, four pairs of quantum mechanics/ molecular mechanics
(QM/MM) Baikal cottoid fish rhodopsin models (with A1 and A2 chromophore)
which successfully reproduce the experimental absorption maxima are prepared
using comparative modeling approach. Analysis of the electrostatic effect of every
amino acid in the retinal chromophore cavity of 4 Å are performed which
reasonably support the hypothesis of the observed mutations inside the retinal
chromophore cavity in the models are involved in the mechanism used by biological
evolution to tune the color of the absorption maxima of the lake Baikal cottoid fish
rhodopsins. Relevant data and results will be presented as a contributed talk.
Reduced Density Matrix Theory in Quantum Chemistry and Physics
David A. Mazziotti
Abstract
Energies and properties of many‐electron molecules can be expressed as a linear functional of
the two‐electron reduced density matrix (2‐RDM). The lecture will discuss recent advances and
applications of 2‐RDM theory including an application to transition‐metal chemistry.
Non-adiabatic current densities, transitions and power absorbed by a molecule in a time-
dependent electromagnetic field
Anirban Mandal and Katharine L. C. Hunt
Department of Chemistry, Michigan State University, East Lansing, MI 48824
The energy of a molecule subject to a time-dependent perturbation separates completely into
adiabatic and non-adiabatic terms, where the adiabatic term reflects the adjustment of the ground
state to the perturbation, while the non-adiabatic term accounts for the transition energy.1 For a
molecule perturbed by a time-dependent transverse electromagnetic field, in this work we show
that the average power absorbed by the molecule is equal to the time rate of change of the non-
adiabatic term in the energy.2 The non-adiabatic term is given by the transition probability to an
excited state k, multiplied by the transition energy from the ground state to k, and then summed
over the excited states. The average power absorbed by the molecule is derived from the integral
over space of the scalar product of the applied electric field and the non-adiabatic current density
induced in the molecule by the field. No net power is absorbed due to the action of the applied
electric field on the adiabatic current density. The work done on the molecule by the applied
field is the time integral of the power absorbed. The result established here shows that work done
on the molecule by the applied field changes the populations of the molecular states. Our results
are based on a perturbed Hamiltonian in the Coulomb gauge. In any arbitrary gauge, the
complete Hamiltonian, including the energy of the electromagnetic field as well as the molecular
energy, is gauge invariant.3
1 A. Mandal and K. L. C. Hunt, J. Chem. Phys. 137, 164109 (2012).
2 A. Mandal and K. L. C. Hunt, J. Chem. Phys. (Submitted).
3 A. Mandal and K. L. C. Hunt, Manuscript in preparation.
This abstract is intended for oral presentation
MWTCC 2015
N2 vs. O2 Adsorption on Open Iron Sites of Fe2(dobdc): An
Electronic Structure Theory Study
Pragya Verma,1 Rémi Maurice,
1,2 Laura Gagliardi,
1,* and Donald G. Truhlar
1,*
1Department of Chemistry, Supercomputing Institute, Nanoporous Materials Genome
Center, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota
55455-0431, USA
2SUBATECH, UMR CNRS 6457, IN2P3/EMN Nantes/Université de Nantes, 4 rue
Alfred Kastler, BP20722, 44307 Nantes Cedex 3, France
*e-mails: [email protected] and [email protected]
The presence of open metal sites and high porosity makes the metal–organic framework
Fe2(dobdc) suitable for separating gaseous mixtures. For example O2 can be adsorbed
more strongly than N2 on Fe2(dobdc), and it can, in principle, be used to separate O2
from air [Bloch et al. J. Am. Chem. Soc. 133, 14814 (2011)]. In this work, we investigate
the differential adsorption of N2 and O2 on Fe2(dobdc) with quantum mechanical
methods applied to a finite-size cluster. The cluster is chosen such that it is large enough
to allow an accurate description of the most important contributions to the binding
enthalpies and small enough that one can perform high-level quantum mechanical
calculations. We use state-of-the-art exchange–correlation functionals as well as wave
function approaches to determine the ground state of the Fe–N2 and Fe–O2 interacting
systems. Our calculations reveal that the ground state structure of the Fe–O2 system has
the dioxygen unit in a triplet spin state ferromagnetically coupled to the high-spin state
(quintet state) of the central iron atom of the cluster. Charge Model 5 (CM5) and LoProp
charge calculations have been performed to determine the partial atomic charges on the
guest molecules (N2 and O2) and the central iron atom of the complex, and these
calculations show that the charge transfer from the open iron(II) site is more important
for O2 than for N2. Furthermore, O2 was calculated to bind more strongly than N2, which
is in agreement with experimental results.
New software for visualization of hyper-spherical coordinates and for 3D-printing of potential energy surfaces: Application to ozone molecule
Alexander Teplukhin and Dmitri Babikov
Chemistry Department, Marquette University, Milwaukee, WI 53201-1881, USA
Quantum molecular dynamics in triatomic systems takes special place in the fundamental chemical theory and in the chemistry education as well, because it allows introducing and studying spectroscopy and chemical reactions using the smallest possible number of atoms. Also, many important gas-phase molecules are triatomic, which makes this topic directly relevant to the real life problems in environmental chemistry, atmospheric chemistry and astrochemistry.
At first sight, there should be nothing special about the choice of vibrational coordinates: it could be valence coordinates (two bond lengths and an angle between bonds) or normal-mode coordinates (represent symmetric stretching, asymmetric stretching and bending). However, neither the valence nor the normal-mode coordinates are employed for accurate numerical studies of triatomics, because the first set results in the extremely complicated Hamiltonian operator, while the second set is an approximation which breaks down at higher levels of vibrational excitation and/or for anharmonic potentials. Jacobi coordinates could be a better choice, but they are arrangement specific: a set of Jacobi coordinates for A + BC arrangement is inappropriate for AB + C arrangement.
This is where the adiabatically-adjusting principal-axes hyper-spherical (APH) coordinates come to scene [1,2]. The Hamiltonian operator in these coordinates is simple, the symmetry is incorporated rigorously, and all three atom arrangements are treated on equal footing. However, one should admit that the APH coordinates are much less popular, compared to the simpler but more limited Jacobi coordinates.
One reason for this is that the formalism of adiabatic adjustment is mathematically involved [1,2] which creates a barrier to understanding, particularly by students at the beginning of their computational research projects. In order to simplify introduction to the APH coordinates we created an interactive desktop application APHDemo [3] that allows seeing a triatomic system on the screen, dragging atoms by mouse from one arrangement to another and watching how the APH coordinates adjust continuously, for example, from the reagent channel to the product channel, through the reaction intermediate. The Jacobi coordinates can also be made visible for comparison, which allows understanding better their drawbacks, and emphasizing advantages of the APH coordinates.
The major area of application of this program is, probably, in the educational process. We created several animations that illustrate typical examples of vibrational dynamics and can be used in the classroom presentation of the APH coordinates. This tool may also be rather handy to those who plan employing the APH coordinates in their research, particularly to graduate students and postdocs.
Another tricky aspect related to APH coordinates is understanding of potential energy surface in these coordinates. In our recent paper [4] we proposed to combine the isoenergy approach with 3D printing technology to create a plastic model of the PES which can be taken into hands and inspected in detail from any perspective (you can examine one for ozone during a poster session). Both APHDemo application and Matlab script to generate an STL file for 3D printer are freely available. References
1. R. T Pack, Chem. Phys. Lett., 108, 333 (1984). 2. R. T Pack and G. A. Parker, J. Chem. Phys., 87, 3888 (1987). 3. A. Teplukhin and D. Babikov, Chem. Phys. Lett., 614, 99 (2014). 4. A. Teplukhin and D. Babikov, J. Chem. Educ., 92(2), 305 (2015).
Bulk and Water-Vapor Interfacial Aqueous
Electrons are Spectroscopically Indistinguishable
Marc P. Coons, Zhi-Qiang You, and John M. Herbert∗
Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
43210
E-mail: [email protected]
Abstract
The vertical detachment energies (VDEs) of the aqueous electron in bulk water
and at the water-vapor interface have been computed using long-range-corrected den-
sity functional theory and mixed quantum/classical molecular dynamics simulations
based on one-electron pseudopotentials. Quantitative agreement with experimental
measurements of VDEs for the bulk species suggests that the chosen methodologies
provide reasonable models for the excess electron. The VDEs of the interfacial elec-
tron are found to be very similar to those in the bulk which is in contrast to the recently
reported value as measured from liquid-jet photoelectron spectroscopy. Our findings
suggest that a new interpretation of the liquid-jet experiments is required to reconcile
experimental and theoretical data. Furthermore our results may have an important im-
pact on the understanding of processes ocurring at aqueous/biological interfaces such
as dissociative electron attachment.
I originally selected my presentation type to be oral, but I would like to
change that. Please consider this for the poster session.
∗To whom correspondence should be addressed
1
Computational Study of Cold Ions Trapped in a Double-Well Potential
Dmytro Shyshlov and Dmitri Babikov
Chemistry Department, Marquette University, Milwaukee, WI 53201
Rigorous computational treatment is developed to study quantum dynamics of cold ions in
a double-well trap. Numerically accurate approach is adopted, that makes no assumption of weak
coupling between the wells, or harmonic approximation for energy spectrum of the double-well
system. The goal is to reproduce, from first principles, the process of efficient energy swaps
between the wells observed in the experiments at NIST [Nature 471, 196 (2011)] and Innsbruck
[Nature 471, 200 (2011)]. The model parameters and the initial conditions are carefully chosen to
reproduce experimental observables. Accurate energies and wave functions of the system are
obtained, and the evolution of motional wave packets on the accurate potential energy surface
(Fig. 1) is studied, which provides new insight. The experimental results are reproduced in detail,
by this model. Explanation of the energy transfer is given in terms of wave packet dynamics in an
asymmetric potential energy well. Surprisingly, it originates in the well-known classical principle:
angle of incidence equals to the angle of reflection, and has nothing to do with quantum tunneling
effect.
Figure 1. Potential energy surface of the system of two Be+ ions in the double-well potential.
CONFERENCE: 2015 Midwest Theoretical Chemistry Conference
DATES: Friday , June 26 – Sunday, June 28, 2015
PLACE: University of Michigan – Ann Arbor , Michigan
---------------------
TITLE : Is the Faster than Expected Diffusion of Small Neutral Solutes in Ionic Liquids Linked to their Polar/Apolar Nature?
PRESENTING AUTHOR : Juan C. Araque
LIST OF ALL AUTHORS WITH AFFILIATION : Juan C. Araque, University of Iowa; Sharad K. Yadav, University of Iowa; Michael Shadeck, Pennsylvania State University; Mark Maroncelli, Pennsylvania State University; and Claudio J. Margulis, University of Iowa.
ABSTRACT:
In a recent article, 1 we described the mechanisms by which diffusion of small neutral solutes in ionic liquids deviates from Stokes-Einstein behavior. This deviation is significantly more pronounced than in the case of conventional solvents.2 We found that small neutral solutes probe ionic liquid regions that are “soft” (of low friction and less polar) and “stiff” (of high electrostriction). The existence of regions of low and high friction can be traced to the charge and apolar structural nature of ionic liquids. Heterogeneous solute diffusional regimes (cage/jump) are thus imposed by the nanoscale solvent structure. Whereas solute displacements are anomalously short in stiff regions (cage regime), they are anomalously large in soft regions (jump regime). Overall, a clear link emerges between ionic liquid structure in the form of polar/apolar duality and deviations from Stokes-Einstein hydrodynamics.
REFERENCES:
1. Araque, J.C., et al., How Is Diffusion of Neutral and Charged Tracers Related to the Structure and
Dynamics of a Room-Temperature Ionic Liquid? Large Deviations from Stokes–Einstein Behavior
Explained. J. Phys. Chem. B, 2015. 119(23): p. 7015-7029.
2. Kaintz, A., et al., Solute Diffusion in Ionic Liquids, NMR Measurements and Comparisons to
Conventional Solvents. J. Phys. Chem. B, 2013. 117(39): p. 11697-11708.
COMMENTS: I would like to give a CONTRIBUTED TALK .
Minimum Energy Conical Intersections Through Graphical
Processing Unit Acceleration of Two Step Methods
B. Scott Fales1
1Department of Chemistry, Michigan State University
12 June 2015
Multireference methods are often used to describe regions of strong nonadiabatic coupling, suchas near a minimum energy conical intersection (MECI). The complete active space self consistentfield (CASSCF) method has long been a standard tool for describing strongly coupled multiref-erence systems, though vertical excitation energies calculated using state averaged CASSCF arenot size intensive and wavefunction convergence is often poor. In pursuit of computationally effi-cient CASSCF alternatives, we have investigated the improved virtual orbital complete active spaceconfiguration interaction (IVO-CASCI)[1][2][3] and the configuration interaction singles natural or-bitals (CISNO-CASCI)[4] methods. Both IVO-CASCI and CISNO-CASCI provide accurate verticalexcitation energies and topographically correct potential energy surfaces (PES) in the MECI regionwhen compared with CASSCF. These methods have been implemented using graphical processingunits (GPUs), an emerging technology which has proven useful for accelerating electronic structuremethods. We demonstrate that multireference CASCI methods can be applied to nanoparticlesby calculating the first several singlet states of systems including a buckeyball (C60), the retinalprecursor β-carotene (C40H56), and a silicon nanoparticle (Si72H68) using active spaces as large as16 electrons in 16 orbitals, using a single NVIDIA K40 GPU and a single core of an Intel Xeon2.40 GHz processor. To facilitate geometry and MECI optimizations of systems approaching thenanoscale, we couple our GPU based methodologies with a numerical optimizer that parallelizesacross multiple nodes, affording us a hierarchical parallelization scheme that scales approximatelylinearly with the number of nodes and GPUs.
I am interested in providing a contributed talk at this years conference, if possible.
References
[1] William J. Hunt and William A. Goddard III. “Excited States of H2 Using Improved VirtualOrbitals”. In: Chem. Phys. Lett. 3 (1969), pp. 414–418.
[2] S. Huzinaga and C. Arnau. “Virtual Orbitals in Hartree-Fock Theory. II”. In: J. Chem. Phys.
54 (1971), pp. 1948–1951.
[3] Davin M. Potts et al. “The improved virtual orbital-complete active space configuration interac-tion method, a ”packageable” efficient ab initio many-body method for describing electronicallyexcited states”. In: J. Chem. Phys. 114 (2001), pp. 2592–2600.
1
[4] Yinan Shu, Edward G. Hohenstein, and Benjamin G. Levine. “Configuration interaction singlesnatural orbitals: An orbital basis for an efficient and size intensive multireference descriptionof electronic excited states”. In: J. Chem. Phys. 142 (2015), p. 024102.
2
Will ice float on water in hybrid density functional
theory world?
Alex P. Gaiduk,† Francois Gygi,‡ and Giulia Galli†
†Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637
‡Department of Computer Science, University of California, Davis, CA 95616
First-principles simulations provide a way to study the properties of wa-ter and aqueous solutions without the need for empirical input. General-ized gradient approximations, commonly used as an engine of first-principlesmolecular dynamics, predict the equilibrium density of water to be lower (0.7–0.9 g/ml) than in the experiment. Hybrid functionals improve the structureand hydrogen bonding in water and could potentially yield better density;however, determining the bulk properties of water with hybrid functionalshas been out of reach due to computational complexity. This work presentsthe first robust determination of density and compressibility of water and iceusing the hybrid functional PBE0. We show that the fraction of Hartree–Fock exchange in PBE0 lowers the density of both water and ice, leading tobetter agreement with the experiment for ice but worse agreement for liquidwater. Inclusion of dispersion interactions on computed molecular-dynamicstrajectories led to a substantial improvement of the PBE0 results for thedensity of liquid water, which, however, resulted to be slightly lower thanthat of ice.
Presentation type: Oral
Active Space Decomposition
Toru Shiozaki
Department of Chemistry, Northwestern University, Evanston, IL 602908, USA.
In this talk I will present an approach to compute diabatic couplings for electron and
energy transfer processes in covalently linked chromophore pairs from an orbital‐optimized
active space decomposition (ASD) method [1]. Our method is based on multi‐configuration
wave functions and is systematically improvable. Applications to triplet transfer processes
in the so‐called Closs systems will be discussed using Marcus theory.
[1] I. Kim, S. M. Parker, and T. Shiozaki, http://arxiv.org/abs/1505.02346 (2015).
Trivalent Metal Loading via Atomic Layer Deposition
Joshua Borycz,b In Soo Kim,
a Ana Platero-Prats,
c Samat Tussupbayev,
b Timothy C.
Wang,d Omar K. Farha,
d,e Joseph T. Hupp,
a,d Laura Gagliardi,
b Karena Chapman,
c
Christopher J. Cramer,*b Alex B. F. Martinson*a
aMaterials Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, Illinois 60439,
USA bDepartment of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of
Minnesota, Minneapolis, Minnesota 55455, United States cX-ray Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, Illinois 60439, USA
dDepartment of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
eDepartment of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
Abstract
Post-synthetic modification of metal organic frameworks (MOFs) can be used to alter
their catalytic function. NU-1000 is a highly stable MOF consisting of Zr6-nodes, which
are reactive with precursors such as trimethylaluminum (AlMe3), trimethylindium
(InMe3), and dimethylaluminum isopropoxide (DMAI) by atomic layer deposition
(ALD). MOFs decorated with Al and In may then be used to catalyze industrially or
environmentally important reactions such as ethane to ethanol conversion. In this work
we used density functional theory to determine the mechanism of addition of the AlMe3,
InMe3, and DMAI precursors to NU-1000 to discern the structure and possible catalytic
utility of these modified MOFs. To confirm our computational results we compared to
experimental X-ray pair distribution function (PDF) data. There is reasonably good
agreement between the proposed computational structures and transition states and
experimental data. Experimental results indicate that a maximum of eight metals add to
each Zr6-node. The computational mechanism predicts that two metals will add to each
face of the Zr6-nodes by reacting with the –OH, -OH2, and µ-OH groups. This leads to a
final structure with eight metals per node with distorted tetrahedral geometries.
MTCC Abstract
Title: LICHEM: A QM/MM Interface for Polarizable Force Fields
Abstract:
We introduce the open source LICHEM software package for QM/MM simulations multipolar and
polarizable force fields. This initial implementation can interface with Gaussian, PSI4, NWChem,
TINKER, and TINKER-HP to enable QM/MM simulations using either the AMOEBA or point-charge
force fields. LICHEM employs wrappers to unmodified QM and MM software packages to perform
geometry optimizations, single-point energies, reaction pathways, and Monte Carlo simulations. We
tested our initial implementation on human DNA polymerase λ and (H2O)n (n=2,3,21) clusters. The
calculations confirm that LICHEM accurately performs high-quality QM/MM simulations and
highlight the importance of polarization.
Authors: Eric G. Kratz and G. Andres Cisneros
Presentation type: Oral presentation preferred if there are still slots available
NOVEL APPROACHES FOR HIGH PERFORMANCE COMPUTATIONAL CHEMISTRY
MARK S. GORDON
IOWA STATE UNIVERSITY
In to enable accurate calculations on large molecules and molecular systems, one
needs to develop novel methods and algorithms to avoid the typically high order
scaling of correlated electronic structure methods. One type of method that can
lower the scaling factor is a fragmentation method, and several of these will be
discussed. A second approach is to develop algorithms that can make efficient use of
novel computer architectures. One such approach will also be discussed.
CH Stretch Vibrations as Probes of Local Environment
Daniel P. Tabor, 1 Timothy S. Zwier,
2 and Edwin L. Sibert III
1
1University of Wisconsin,
2Purdue University
The CH stretch region is an interesting candidate as a probe of structure and local environment.
The functional groups are ubiquitous and their vibration spectra exhibit a surprising sensitivity to
molecular structure. In this talk we review our theoretical model Hamiltonian [J. Chem. Phys.
138 064308 (2013)] for describing vibrational spectra associated with the CH stretch of CH2
groups and then describe an extension of it to molecules containing methyl and methoxy groups.
Results are compared to gas phase, conformer specific infrared spectroscopy of a set of
molecules that highlight the role of symmetry and environment. The curvilinear local-mode
Hamiltonian predicts most of the major spectral features considered in this study and provides
insights into mode mixing. We conclude by considering how the CH stretch spectrum of
cyclohexane is substantially modified when it forms a complex with a series of alkali metals and
what these spectra tell about the structure of the complex.
Completely Renormalized Coupled-Cluster Calculations for Bond Breaking Using Unrestricted Hartree-Fock References
Jared A. Hansen,1 Piotr Piecuch,1,2 and Jun Shen1
1Department of Chemistry, Michigan State University, East Lansing, MI 48824, U.S.A.
2Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, U.S.A.
The popular coupled-cluster CCSD(T) approach works well for molecules near their equilibrium geometries, but it fails to describe potential energy surfaces (PESs) along bond breaking coordinates and biradicals if the restricted Hartree-Fock (RHF) determinant is used as a reference. One approach to address this concern is to use the unrestricted Hartree-Fock (UHF) determinant as the reference wave function in CCSD(T) computations. While this eliminates the unphysical characteristics of the RHF-based CCSD(T) PESs in the bond breaking regions, it introduces other issues, such as spin-contamination and non-analytic behavior of the resulting surfaces. Another way in which the failures of RHF-based CCSD(T) calculations can be addressed is by turning to the completely renormalized coupled-cluster (CR-CC) methods, such as CR-CCSD(T) and its more recent, rigorously size extensive, counterpart termed CR-CC(2,3). These approaches and their higher-order extensions provide an accurate description of biradical and single bond-breaking situations using RHF references, but the question remains as to whether or not the UHF-based CR-CC approaches, especially CR-CC(2,3), can further improve their RHF-based counterparts, particularly for single bond breaking into open-shell fragments on singlet PESs. To address this question, we present the UHF-based CR-CCSD(T) and CR-CC(2,3) results for bond breaking in the HF, F2, H2O2, and C2H6 molecules, comparing them with the exact, full configuration interaction, and full CCSDT data and the results of the RHF-based CR-CCSD(T) and CR-CC(2,3) calculations. We show that, unlike the CCSD(T) approach, which is very sensitive to the type of the reference determinant employed in the calculations, the CR-CC approximations provide a robust description regardless of the reference type (RHF or UHF), with the spin-adapted RHF-based CR-CC(2,3) results being most accurate for the bond breaking cases examined in this work.
Accurate Prediction of Lattice Energies of Molecular Crystals with Extended
Symmetry-Adapted Perturbation Theory
Ka Un Lao∗and John M. Herbert
Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
The efficient fragment-based method (XSAPT) developed by our group with chemical accuracyfor non-covalent interactions in molecular clusters has been extended to molecular crystals underperiodic boundary conditions (PBC) by incorporating long-range electrostatic interactions usingEwald-summation. The PBC-XSAPT method affords lattice energies within experimental uncer-tainty for a variety of molecular crystals, such as solid NH3, CO2, H2O, and C6H6. Crystallineoxalyl dihydrazide with five experimentally known polymorphs is a challenging system for theoret-ical crystal modeling since the polymorph energy ordering is governed by subtle balances betweendifferent kinds of interactions. Dispersion-corrected density functional approximations (DFT-D)fails to reproduce experimental observations. Nevertheless, our PBC-XSAPT method agrees withthe available experimental ordering. The “embarrassingly parallelizable” property of XSAPT makeit efficient enough to be applied to molecular crystals containing numerous monomer units. Further-more, the PBC-XSAPT interaction energy can be decomposed into physically meaningful energycomponents and such understanding is very useful for rational design of molecular crystals.
∗ I would like to give a contributed talk
Nuclear Quantum Effects are Important in Calculating the Electronic Spectrum of 9-Methylguanine
Yu Kay Lawa and Ali A. Hassanalib
Department of Science, Indiana University East, Richmond, INa and Condensed Matter Physics Section, The Abdus Salaam International Center for Theoretical Physics, Trieste, Italyb
Conformations of 9-methylguanine were sampled using the Cornell et al force field, ab initio Born-Oppenheimer molecular dynamics (BOMD)
simulation with classical nuclei and 9-methylguanine using a path-integral treatment of nuclear quantum effects (NQE). These conformations were
then used to calculate the heterogeneously-broadened absorption spectrum of 9-methylguanine using TD-DFT using the Franck-Condon approximation. We show that incorporation of nuclear quantum effects in
conformational sampling significantly broadens the distribution of bond lengths in 9-methylguanine, leading to significant broadening to the red-end of the calculated absorption spectrum, leading to much improved
correspondence with the experimental spectrum for this molecule. This suggests significant conformational freedom can be attributed to the
presence of quantum effects on the nuclei, something that is often neglected in conformational sampling. The role of the inclusion of water as part of the model in TD-DFT calculations, at the macroscopic level, was
largely found to modulate the transition dipole moments of the guanine base rather than the excitation energies; perturbations due to the
presence of water varied between different conformers, leading to a cancellation of their overall effect on the bulk absorption spectrum.
Conjugation in Aromatic S-Nitrosothiols: Interaction of a π-
bond and –SNO Moiety
Matthew Flister and Qadir K. Timerghazin*
Department of Chemistry, Marquette University
Milwaukee, WI 53233
The development of new S-nitrosothiols (RSNOs) is key to the advancement of a
growing field of study in the biochemistry of nitric oxide (NO) due to the ubiquitous
nature of RSNOs in living organisms. These thiol derivatives can undergo homolytic
dissociation of the S–N bond releasing NO and possibly nitroxyl HNO, small molecules
with significant impact in many biological processes. While progress has been made in
biological applications of NO, few synthetic or endogenous RSNOs have emerged with
controlled and tunable release of NO. Moreover, many stable synthetic RSNOs involve
bulky substituent groups inducing stability of the –SNO group but preventing the
controlled release of NO. Study of substituent effects on the –SNO group should serve as
a reliable means for systematic development of new RSNOs. We have previously studied
PhSNO as a simple scaffold to use in substituent study. However, due to the non-planar
geometry of PhSNO and limited conjugation between the aromatic ring and –SNO group,
it is still unclear as to the exact effect of conjugation between a π-bond or π-system and
an RSNO. In this contribution, we will detail a thorough investigation of the simplest
form of RSNO in proximity to a π-bond or π-system, vinyl-SNO (VinSNO). We will
discuss the complex electronic structure of VinSNO using results from natural bond
orbital (NBO) calculations with special emphasis on the donor/acceptor interactions
between the π-bond and –SNO group of VinSNO. Furthermore, we will provide
comparison between VinSNO and PhSNO toward a broader understanding of the whole
class of aromatic RSNOs.
Reduced-scaling electronic structure theory approaches for simulating
responsive organic materials
Keith A. Werling and Daniel S. Lambrecht
University of Pittsburgh, Department of Chemistry, 219 Parkman Ave, Pittsburgh PA, 15206
We present a hierarchy of hybrid approaches for embedded many-body expansions combined
with local approximations to enable expedited irst principles calculations of organic materials
properties. We demonstrate calculations of deformation in response to external electric and
mechanical stimuli within this framework, as is required to assess applications as responsive
materials (e.g. piezoelectric sensors, shape-shifting electromechanical materials). Treating
these crystalline or semi-crystalline molecular materials under the inluence of external
perturbations requires a balanced description of subtle intermolecular forces. We show that
the presented approaches provide CCSD(T)-quality results while appealing with reduced
scaling with system size as low as O(N) as well as embarrassing parallelism. Diferent variants
for the many-body embedding, ranging from point charges to quantum mechanical embedding,
are analyzed with respect to the quality of the results and computational eiciency. We then
present applications of our approaches to inding improved hydrogen-bonded organic
piezoelectric materials [1-2].
[1] K. A. Werling, G. R. Hutchison, and D. S. Lambrecht, “Piezoelectric Efects of Applied
Electric Fields on Hydrogen-Bond Interactions: First-Principles Electronic Structure
Investigation of Weak Electrostatic Interactions”, J. Phys. Chem. Lett. 4, 1365-1370 (2013).
[2] K. A. Werling, M. Griin, G. R. Hutchison, and D. S. Lambrecht, "Piezoelectric Hydrogen
Bonding: Computational Screening for a Design Rationale", J. Phys. Chem. A 118, 7404-7410
(2014).
An approach to pure-sampling quantum Monte Carlo.
Egor Ospadov and Stuart M. Rothsteina,
Departments of Chemistry and Physics,
Brock University,
St. Catharines, ON L2S 3A1 CANADA
Diffusion quantum Monte Carlo, the most widely-used quantum Monte Carlo algorithm, samples from
ΨΦ0. This so-called “mixed distribution” is the product of an inputted importance sampling function (Ψ)
and the unknown “exact” ground-state wave function (Φ0), which is exact, save for the mismatch of its
nodal hypersurface with that of the truly exact wave function. The importance sampling function Ψ
substantially biases physical properties represented by operators that commute with the position operator,
such as the dipole moment. The objective of pure-sampling quantum Monte Carlo is to remove Ψ from the
sampled distribution, to sample from the so-called “pure distribution”, |Φ0|2, and thus to calculate physical
properties that are independent of the importance sampling function being employed in the calculation.
We describe a pure-sampling quantum Monte Carlo algorithm that achieves this objective [EO and SMR, J.
Chem. Phys. 142, 024114 (2015)] Our algorithm is implemented by systematically increasing an
algorithmic parameter until the calculations converge to statistically equivalent values. Thereby one
unambiguously determines values for the ground-state energy, static electrical response properties and
other one-electron expectation values. These quantities are free from biases that plague other approaches in
the literature: importance sampling bias, population control bias, time-step bias, extrapolation-model bias,
and the finite-field approximation. Applications of the algorithm to a variety of molecules are described,
with some emphasis on technical challenges poised by large molecules.
______________________________________________________ a [email protected]
SMR should like to give a contributed talk.
Performance and Energy Efficiency of Quantum Chemistry Algorithms on Modern Computer Architectures
Kristopher Keiperta. Gaurav Mitra
b, Vaibhav Sunriyal
a, Sarom S. Leang
a, Masha Sosonkina
c,
Alistair Rendellb, and Mark S. Gordon
a
aDepartment of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111,United States
bResearch School of Computer Science, Australian National University, Acton ACT 0200,Australia
cDepartment of Modeling and Simulation, Old Dominion University, Norfolk, VA 23529 United States
The energy costs associated with cooling and powering a high performance supercomputer system usually surpass
the initial equipment costs over 3-4 years of use. Poor energy efficiency of modern computer hardware is the most
significant barrier to reaching exascale computing. Development of significantly more efficient hardware designs and
software algorithms is necessary to continue advancement of computationally feasible chemical system sizes which can be
studied with accurate ab initio quantum chemistry algorithms . Most mobile consumer devices use RISC-based ARM CPUs
that are designed for low power consumption. Recent improvements in mobile computing performance have enabled use of
ARM CPUs for high performance scientific applications. Modern CISC-based architectures such as Haswell x86 have been
designed with a focus on energy efficiency as well. The performance and energy-to-solution for a variety of quantum
chemistry algorithms in the GAMESS quantum chemistry application have been measured for ARM32, ARM64, and
Haswell x86 architectures. The Haswell x86 system is shown to have 2-4x better performance than the ARM systems for all
benchmark cases, while having worse energy efficiency than ARM64 for some parallel algorithms. The ARM32 device is
more energy efficient than ARM32 and ARM64 for all benchmark cases.
Note: I would like to present this orally.
Midwest Theoretical Chemistry Conference Abstract Title: Using Range-Separated Hybrid Density Functional Theory for Rational Design of Organic Optoelectronic Devices Authors: Heidi Hendrickson Zilong Zheng, Francis Devine, Shaohui Zheng, Eitan Geva, Barry Dunietz Abstract:
A fundamental understanding of charge separation in organic materials is necessary for the rational design of optoelectronic applications. Computational approaches provide fundamental insights into related processes, which in turn guide the synthesis of novel optoelectronic materials. Conventional density functional theory (DFT) methods have been known to fail in accurately characterizing frontier orbital gaps and charge transfer states in molecular systems. We address these shortcomings by implementing an optimally-tuned range-separated hybrid (OT-RSH) functional approach within DFT and time-dependent (TD) DFT. Our work particularly addresses the effect of the surrounding environment on fundamental molecular properties such as ionization potential (IP), electron affinity (EA), and charge transfer excitation energies. Specifically, we have investigated the spurious agreement between thin film IP/EA measurements and gas-phase frontier orbital energies calculated with widely-used density functionals. We show that both gas-phase and environmentally-corrected RSH-DFT frontier orbital energies properly correspond to gas-phase and thin-film experimental measurements, respectively, for a set of organic semiconducting molecules.
We also benchmark the RSH functionals in describing charge transfer excitation by using a model ethene dimer and silsesquioxane molecules currently investigated as candidates for building blocks in photovoltaic applications. In order to account for complex environmental effects on charge transfer energies in silsesquioxane molecules, a protocol combining charge-constrained DFT, a polarizable continuum solvent model, and RSH TDDFT was tested and validated against experimental measurements. The protocol provides a way to understand charge transfer within complex environments for molecules used in photovoltaic applications. Current work is focused on extending this method to various silsesquioxane systems.
Evolving Fluorophores for Organic Light Emitting Diodes
Yinan Shu and Benjamin G. Levine
Department of Chemistry, Michigan State University, East Lansing, MI 48824
Organic light-emitting diodes (OLEDs) are the basis for low-cost, high-resolution flat panel displays.
Recently, Adachi and co-workers developed highly efficient OLEDs which employ thermally activated
delayed fluorescence (TADF) to enhance the luminescence quantum yield. TADF is most efficient when
the gap between S1 and T1 is small and the S1-S0 transition dipole moment is large, but these two properties
are difficult to achieve simultaneously. By taking advantage of parallel graphics processing unit (GPU)
computing and genetic algorithms, we are able to pre-screen a large set of possible candidates and evolve
these molecules towards the desired properties. The fitness of each candidate for TADF is estimated using
GPU-accelerated density functional and time-dependent density functional calculations. The set of optimal
candidates identified in our study includes some molecules known to exhibit TADF and others that have
not been reported in the literature.
Dear Organnizer:
I would like to apply for oral presentation.