Satyender Goel | Northwestern University (original) (raw)

Papers by Satyender Goel

Journal of Physical Chemistry Letters, 2010

The influence of ligands on electronic structure of small gold clusters (Au 2 , Au 4 ) has been i... more The influence of ligands on electronic structure of small gold clusters (Au 2 , Au 4 ) has been investigated by density functional theory (DFT). Specifically, we study the effect of bonding of four donor ligands (NH 3 , NMe 3 , PH 3 , and PMe 3 ) on cluster geometries and energetics in gas phase and in solution. Performance of five generations of DFT functionals and five different basis sets is assessed. Our results benchmark the importance of the DFT functional model and polarization functions in the basis set for calculations of ligated gold cluster systems. We obtain NMe 3 ≈ NH 3 < PH 3 < PMe 3 order of ligand binding energies and observe shallow potential energy surfaces in all molecules. The latter is likely to lead to a conformational freedom in larger clusters with many ligands in solution at ambient conditions. The study suggests appropriate quantum-chemical methodology to reliably model small noble metal clusters in a realistic ligand environment typically present in experiments.

Journal of the American Medical Informatics Association : JAMIA, Jan 23, 2015

To design and implement a tool that creates a secure, privacy preserving linkage of electronic he... more To design and implement a tool that creates a secure, privacy preserving linkage of electronic health record (EHR) data across multiple sites in a large metropolitan area in the United States (Chicago, IL), for use in clinical research. The authors developed and distributed a software application that performs standardized data cleaning, preprocessing, and hashing of patient identifiers to remove all protected health information. The application creates seeded hash code combinations of patient identifiers using a Health Insurance Portability and Accountability Act compliant SHA-512 algorithm that minimizes re-identification risk. The authors subsequently linked individual records using a central honest broker with an algorithm that assigns weights to hash combinations in order to generate high specificity matches. The software application successfully linked and de-duplicated 7 million records across 6 institutions, resulting in a cohort of 5 million unique records. Using a manually...

Current Cardiovascular Risk Reports, 2014

Over the past decade, there has been explosive growth in the amount of healthcare-related data ge... more Over the past decade, there has been explosive growth in the amount of healthcare-related data generated and interest in harnessing this data for research purposes and informing public policy. Outside of healthcare, specialized software has been developed to tackle the problems that voluminous data creates, and these techniques could be applicable in several areas of cardiovascular research. Cardiovascular risk analysis may benefit from the inclusion of patient genetic and health record data, while cardiovascular epidemiology could benefit from crowd-sourced environmental data. Some of the most significant advances may come from the ability to predict and respond to events in real-time-such as assessing the impact of new public policy at the community level on a weekly basis through electronic health records or monitoring a patient's cardiovascular health remotely with a smartphone.

Lecture Notes in Computer Science, 2009

Nanoelectronics and photonics applications of single wall carbon nanotubes (SWNT) are feasible on... more Nanoelectronics and photonics applications of single wall carbon nanotubes (SWNT) are feasible only if SWNTs have specific chirality. The knowledge of the detailed mechanism for SWNT synthesis would allow one to optimize the chemical vapor deposition (CVD) process and may help to gain control over selectivity of SWNT synthesis. While it is not probably feasible to study this mechanism experimentally, it could be analyzed using molecular simulations. Here we propose multiscale computer modeling of CVD process. High theory level can be used for di-and tri-atomic fragments, in order to generate parameters for bond order force field. In turn, force field simulations will be used to characterize the chemical origin and thermochemical properties of the intermediates and transition states. This will allow predicting the rate constants for the elementary steps, which are then used in kinetic Monte Carlo simulations to describe SWNT growth at realistic time scales.

Lecture Notes in Computer Science, 2009

A clear advantage of broken symmetry (BS) unrestricted density functional theory DFT is qualitati... more A clear advantage of broken symmetry (BS) unrestricted density functional theory DFT is qualitatively correct description of bond dissociation process, but its disadvantage is that spin-polarized Slater determinant is no longer a pure spin state (a.k.a. spin contamination). We propose a new approach to eliminate the spin-contamination, based on canonical Natural Orbitals (NO). We derive an expression to extract the energy of the pure singlet state given in terms of energy of BS DFT solution, the occupation number of the bonding NO, and the energy of the higher state built on these bonding and antibonding NOs (as opposed to self-consistent Kohn-Sham orbitals). Thus, unlike spincontamination correction schemes by Noodleman and Yamaguchi, spincorrection is introduced for each correlated electron pair individually and thus expected to give more accurate results. We validate this approach on two examples, a simple diatomic H 2 and transition metal hydride MnH.

2009 Third International Conference on Quantum, Nano and Micro Technologies, 2009

Single wall carbon nanotubes (SWNT) have unique properties that make them potentially useful in w... more Single wall carbon nanotubes (SWNT) have unique properties that make them potentially useful in wide variety of applications in nanoelectronics. However, these applications are feasible only if SWNTs have specific chirality. Therefore optimization of experimental conditions for Chemical Vapor Deposition (CVD) growth of SWNT in order to increase its selectivity is of great practical importance. This rational optimization is impossible without knowledge of mechanistic kinetics of CVD. It is not probably feasible to extract the information on mechanism for SWNT synthesis from experimental data. The chemical origin of the reaction barriers and intermediates, however, could be analyzed using molecular simulations. Here we propose multiscale computer modeling of CVD process. Our approach is to extract the structure of the intermediates from molecular dynamics trajectories, conduct the transition state search, predict the free energy activation barriers, build the kinetic model of the growth process, and implement it in kinetic Monte Carlo algorithm to predict the optimal experimental conditions necessary to produce desired chirality of SWNT.

Journal of the American Medical Informatics Association : JAMIA

The Chicago Area Patient-Centered Outcomes Research Network (CAPriCORN) represents an unprecedent... more The Chicago Area Patient-Centered Outcomes Research Network (CAPriCORN) represents an unprecedented collaboration across diverse healthcare institutions including private, county, and state hospitals and health systems, a consortium of Federally Qualified Health Centers, and two Department of Veterans Affairs hospitals. CAPriCORN builds on the strengths of our institutions to develop a cross-cutting infrastructure for sustainable and patient-centered comparative effectiveness research in Chicago. Unique aspects include collaboration with the University HealthSystem Consortium to aggregate data across sites, a centralized communication center to integrate patient recruitment with the data infrastructure, and a centralized institutional review board to ensure a strong and efficient human subject protection program. With coordination by the Chicago Community Trust and the Illinois Medical District Commission, CAPriCORN will model how healthcare institutions can overcome barriers of dat...

The Journal of Physical Chemistry C, 2012

Ligand influence on the excited state structure of small neutral gold clusters (Au 2 and Au 4 ) h... more Ligand influence on the excited state structure of small neutral gold clusters (Au 2 and Au 4 ) has been investigated using Time Dependent Density Functional Theory. We study in detail the absorption profile of bare and ligated small gold clusters in solution modeled with Polarizable Continuum Model. Performance of CAM-B3LYP and TPSS DFT functionals combined with TZVP basis set has been assessed. We found that ligands substantially modify the excited state structure of clusters by eliminating low-lying optically inactive excited states. Depending on the ligand environment, the cluster may gain significant fluorescence efficiency. Our results suggest that small gold clusters ligated with amines will have better fluorescence potential compared to those ligated with phosphine or thiol ligands, in agreement with preliminary experimental data. TPSS fails to describe excited state structure of ligated clusters due to spurious charge-transfer states, thus highlighting the necessity of choosing appropriate quantum-chemistry model for correct excited state description.

The Journal of Physical Chemistry Letters, 2010

The influence of ligands on electronic structure of small gold clusters (Au 2 , Au 4 ) has been i... more The influence of ligands on electronic structure of small gold clusters (Au 2 , Au 4 ) has been investigated by density functional theory (DFT). Specifically, we study the effect of bonding of four donor ligands (NH 3 , NMe 3 , PH 3 , and PMe 3 ) on cluster geometries and energetics in gas phase and in solution. Performance of five generations of DFT functionals and five different basis sets is assessed. Our results benchmark the importance of the DFT functional model and polarization functions in the basis set for calculations of ligated gold cluster systems. We obtain NMe 3 ≈ NH 3 < PH 3 < PMe 3 order of ligand binding energies and observe shallow potential energy surfaces in all molecules. The latter is likely to lead to a conformational freedom in larger clusters with many ligands in solution at ambient conditions. The study suggests appropriate quantum-chemical methodology to reliably model small noble metal clusters in a realistic ligand environment typically present in experiments.

Journal of Molecular Modeling, 2012

The stable geometries and atomization energies for the clusters Ni n (n=2-5) are predicted with a... more The stable geometries and atomization energies for the clusters Ni n (n=2-5) are predicted with all-electron density functional theory (DFT), using the BMK hybrid functional and a Gaussian basis set. Possible isomers and several spin states of these nickel clusters are considered systematically. The ground spin state and the lowest energy isomers are identified for each cluster size. The results are compared to available experimental and other theoretical data. The molecular orbitals of the largest cluster are plotted for all spin states. The relative stabilities of these states are interpreted in terms of superatom orbitals and no-pair bonding.

The Journal of Chemical Physics, 2008

We investigate gas-phase neutral and cationic hydrides formed by 3d transition metals from Sc to ... more We investigate gas-phase neutral and cationic hydrides formed by 3d transition metals from Sc to Cu with density functional theory ͑DFT͒ methods. The performance of two exchange-correlation functionals, Boese-Martin for kinetics ͑BMK͒ and Tao-Perdew-Staroverov-Scuseria ͑TPSS͒, in predicting bond lengths and energetics, electronic structures, dipole moments, and ionization potentials is evaluated in comparison with available experimental data. To ensure a unique self-consistent field ͑SCF͒ solution, we use stability analysis, Fermi smearing, and continuity analysis of the potential energy curves. Broken-symmetry approach was adapted in order to get the qualitatively correct description of the bond dissociation. We found that on average BMK predicted values of dissociation energies and ionization potentials are closer to experiment than those obtained with high level wave function theory methods. This agreement deteriorates quickly when the fraction of the Hartree-Fock exchange in DFT functional is decreased. Natural bond orbital ͑NBO͒ population analysis was used to describe the details of chemical bonding in the systems studied. The multireference character in the wave function description of the hydrides is reproduced in broken-symmetry DFT description, as evidenced by NBO analysis. We also propose a new scheme to correct for spin contamination arising in broken-symmetry DFT approach. Unlike conventional schemes, our spin correction is introduced for each spin-polarized electron pair individually and therefore is expected to yield more accurate energy values. We derive an expression to extract the energy of the pure singlet state from the energy of the broken-symmetry DFT description of the low spin state and the energies of the high spin states ͑pentuplet and two spin-contaminated triplets in the case of two spin-polarized electron pairs͒. The high spin states are build with canonical natural orbitals and do not require SCF convergence.

The computational description of the catalytic processes on the surface of transition metals (TMs... more The computational description of the catalytic processes on the surface of transition metals (TMs) requires methods capable of accurate prediction of the bond forming and breaking between the atoms of metal and other elements. In our previous report [Goel and Masunov, J Chem Phys, 129, 214302, 2008], we studied TM hydrides and found that Boese-Martin functional for kinetics (BMK) combined with broken symmetry approach described dissociation process more accurately than multireference wavefunction theory (WFT) methods and some other functionals. Here, we investigate the binding energy, geometry, electronic structure, and potential energy curves for diatomic TM carbides using several exchange-correlation functionals. The functionals that include explicit dependence on the kinetic energy density (s-functionals) are considered, among others. We have found M05-2x performance to be the best, followed by BMK, when compared with experimental and high level WFT energetics. This agreement deteriorates quickly for other functionals when the fraction of the Hartree-Fock exchange is decreased. Scalar relativistic corrections yield mixed results for bond lengths and bond energies. The natural bond orbital analysis provides useful insight in description of stable spin state over others in these diatomics.

Journal of Physical Chemistry Letters, 2010

The influence of ligands on electronic structure of small gold clusters (Au 2 , Au 4 ) has been i... more The influence of ligands on electronic structure of small gold clusters (Au 2 , Au 4 ) has been investigated by density functional theory (DFT). Specifically, we study the effect of bonding of four donor ligands (NH 3 , NMe 3 , PH 3 , and PMe 3 ) on cluster geometries and energetics in gas phase and in solution. Performance of five generations of DFT functionals and five different basis sets is assessed. Our results benchmark the importance of the DFT functional model and polarization functions in the basis set for calculations of ligated gold cluster systems. We obtain NMe 3 ≈ NH 3 < PH 3 < PMe 3 order of ligand binding energies and observe shallow potential energy surfaces in all molecules. The latter is likely to lead to a conformational freedom in larger clusters with many ligands in solution at ambient conditions. The study suggests appropriate quantum-chemical methodology to reliably model small noble metal clusters in a realistic ligand environment typically present in experiments.

Journal of the American Medical Informatics Association : JAMIA, Jan 23, 2015

To design and implement a tool that creates a secure, privacy preserving linkage of electronic he... more To design and implement a tool that creates a secure, privacy preserving linkage of electronic health record (EHR) data across multiple sites in a large metropolitan area in the United States (Chicago, IL), for use in clinical research. The authors developed and distributed a software application that performs standardized data cleaning, preprocessing, and hashing of patient identifiers to remove all protected health information. The application creates seeded hash code combinations of patient identifiers using a Health Insurance Portability and Accountability Act compliant SHA-512 algorithm that minimizes re-identification risk. The authors subsequently linked individual records using a central honest broker with an algorithm that assigns weights to hash combinations in order to generate high specificity matches. The software application successfully linked and de-duplicated 7 million records across 6 institutions, resulting in a cohort of 5 million unique records. Using a manually...

Current Cardiovascular Risk Reports, 2014

Over the past decade, there has been explosive growth in the amount of healthcare-related data ge... more Over the past decade, there has been explosive growth in the amount of healthcare-related data generated and interest in harnessing this data for research purposes and informing public policy. Outside of healthcare, specialized software has been developed to tackle the problems that voluminous data creates, and these techniques could be applicable in several areas of cardiovascular research. Cardiovascular risk analysis may benefit from the inclusion of patient genetic and health record data, while cardiovascular epidemiology could benefit from crowd-sourced environmental data. Some of the most significant advances may come from the ability to predict and respond to events in real-time-such as assessing the impact of new public policy at the community level on a weekly basis through electronic health records or monitoring a patient's cardiovascular health remotely with a smartphone.

Lecture Notes in Computer Science, 2009

Nanoelectronics and photonics applications of single wall carbon nanotubes (SWNT) are feasible on... more Nanoelectronics and photonics applications of single wall carbon nanotubes (SWNT) are feasible only if SWNTs have specific chirality. The knowledge of the detailed mechanism for SWNT synthesis would allow one to optimize the chemical vapor deposition (CVD) process and may help to gain control over selectivity of SWNT synthesis. While it is not probably feasible to study this mechanism experimentally, it could be analyzed using molecular simulations. Here we propose multiscale computer modeling of CVD process. High theory level can be used for di-and tri-atomic fragments, in order to generate parameters for bond order force field. In turn, force field simulations will be used to characterize the chemical origin and thermochemical properties of the intermediates and transition states. This will allow predicting the rate constants for the elementary steps, which are then used in kinetic Monte Carlo simulations to describe SWNT growth at realistic time scales.

Lecture Notes in Computer Science, 2009

A clear advantage of broken symmetry (BS) unrestricted density functional theory DFT is qualitati... more A clear advantage of broken symmetry (BS) unrestricted density functional theory DFT is qualitatively correct description of bond dissociation process, but its disadvantage is that spin-polarized Slater determinant is no longer a pure spin state (a.k.a. spin contamination). We propose a new approach to eliminate the spin-contamination, based on canonical Natural Orbitals (NO). We derive an expression to extract the energy of the pure singlet state given in terms of energy of BS DFT solution, the occupation number of the bonding NO, and the energy of the higher state built on these bonding and antibonding NOs (as opposed to self-consistent Kohn-Sham orbitals). Thus, unlike spincontamination correction schemes by Noodleman and Yamaguchi, spincorrection is introduced for each correlated electron pair individually and thus expected to give more accurate results. We validate this approach on two examples, a simple diatomic H 2 and transition metal hydride MnH.

2009 Third International Conference on Quantum, Nano and Micro Technologies, 2009

Single wall carbon nanotubes (SWNT) have unique properties that make them potentially useful in w... more Single wall carbon nanotubes (SWNT) have unique properties that make them potentially useful in wide variety of applications in nanoelectronics. However, these applications are feasible only if SWNTs have specific chirality. Therefore optimization of experimental conditions for Chemical Vapor Deposition (CVD) growth of SWNT in order to increase its selectivity is of great practical importance. This rational optimization is impossible without knowledge of mechanistic kinetics of CVD. It is not probably feasible to extract the information on mechanism for SWNT synthesis from experimental data. The chemical origin of the reaction barriers and intermediates, however, could be analyzed using molecular simulations. Here we propose multiscale computer modeling of CVD process. Our approach is to extract the structure of the intermediates from molecular dynamics trajectories, conduct the transition state search, predict the free energy activation barriers, build the kinetic model of the growth process, and implement it in kinetic Monte Carlo algorithm to predict the optimal experimental conditions necessary to produce desired chirality of SWNT.

Journal of the American Medical Informatics Association : JAMIA

The Chicago Area Patient-Centered Outcomes Research Network (CAPriCORN) represents an unprecedent... more The Chicago Area Patient-Centered Outcomes Research Network (CAPriCORN) represents an unprecedented collaboration across diverse healthcare institutions including private, county, and state hospitals and health systems, a consortium of Federally Qualified Health Centers, and two Department of Veterans Affairs hospitals. CAPriCORN builds on the strengths of our institutions to develop a cross-cutting infrastructure for sustainable and patient-centered comparative effectiveness research in Chicago. Unique aspects include collaboration with the University HealthSystem Consortium to aggregate data across sites, a centralized communication center to integrate patient recruitment with the data infrastructure, and a centralized institutional review board to ensure a strong and efficient human subject protection program. With coordination by the Chicago Community Trust and the Illinois Medical District Commission, CAPriCORN will model how healthcare institutions can overcome barriers of dat...

The Journal of Physical Chemistry C, 2012

Ligand influence on the excited state structure of small neutral gold clusters (Au 2 and Au 4 ) h... more Ligand influence on the excited state structure of small neutral gold clusters (Au 2 and Au 4 ) has been investigated using Time Dependent Density Functional Theory. We study in detail the absorption profile of bare and ligated small gold clusters in solution modeled with Polarizable Continuum Model. Performance of CAM-B3LYP and TPSS DFT functionals combined with TZVP basis set has been assessed. We found that ligands substantially modify the excited state structure of clusters by eliminating low-lying optically inactive excited states. Depending on the ligand environment, the cluster may gain significant fluorescence efficiency. Our results suggest that small gold clusters ligated with amines will have better fluorescence potential compared to those ligated with phosphine or thiol ligands, in agreement with preliminary experimental data. TPSS fails to describe excited state structure of ligated clusters due to spurious charge-transfer states, thus highlighting the necessity of choosing appropriate quantum-chemistry model for correct excited state description.

The Journal of Physical Chemistry Letters, 2010

The influence of ligands on electronic structure of small gold clusters (Au 2 , Au 4 ) has been i... more The influence of ligands on electronic structure of small gold clusters (Au 2 , Au 4 ) has been investigated by density functional theory (DFT). Specifically, we study the effect of bonding of four donor ligands (NH 3 , NMe 3 , PH 3 , and PMe 3 ) on cluster geometries and energetics in gas phase and in solution. Performance of five generations of DFT functionals and five different basis sets is assessed. Our results benchmark the importance of the DFT functional model and polarization functions in the basis set for calculations of ligated gold cluster systems. We obtain NMe 3 ≈ NH 3 < PH 3 < PMe 3 order of ligand binding energies and observe shallow potential energy surfaces in all molecules. The latter is likely to lead to a conformational freedom in larger clusters with many ligands in solution at ambient conditions. The study suggests appropriate quantum-chemical methodology to reliably model small noble metal clusters in a realistic ligand environment typically present in experiments.

Journal of Molecular Modeling, 2012

The stable geometries and atomization energies for the clusters Ni n (n=2-5) are predicted with a... more The stable geometries and atomization energies for the clusters Ni n (n=2-5) are predicted with all-electron density functional theory (DFT), using the BMK hybrid functional and a Gaussian basis set. Possible isomers and several spin states of these nickel clusters are considered systematically. The ground spin state and the lowest energy isomers are identified for each cluster size. The results are compared to available experimental and other theoretical data. The molecular orbitals of the largest cluster are plotted for all spin states. The relative stabilities of these states are interpreted in terms of superatom orbitals and no-pair bonding.

The Journal of Chemical Physics, 2008

We investigate gas-phase neutral and cationic hydrides formed by 3d transition metals from Sc to ... more We investigate gas-phase neutral and cationic hydrides formed by 3d transition metals from Sc to Cu with density functional theory ͑DFT͒ methods. The performance of two exchange-correlation functionals, Boese-Martin for kinetics ͑BMK͒ and Tao-Perdew-Staroverov-Scuseria ͑TPSS͒, in predicting bond lengths and energetics, electronic structures, dipole moments, and ionization potentials is evaluated in comparison with available experimental data. To ensure a unique self-consistent field ͑SCF͒ solution, we use stability analysis, Fermi smearing, and continuity analysis of the potential energy curves. Broken-symmetry approach was adapted in order to get the qualitatively correct description of the bond dissociation. We found that on average BMK predicted values of dissociation energies and ionization potentials are closer to experiment than those obtained with high level wave function theory methods. This agreement deteriorates quickly when the fraction of the Hartree-Fock exchange in DFT functional is decreased. Natural bond orbital ͑NBO͒ population analysis was used to describe the details of chemical bonding in the systems studied. The multireference character in the wave function description of the hydrides is reproduced in broken-symmetry DFT description, as evidenced by NBO analysis. We also propose a new scheme to correct for spin contamination arising in broken-symmetry DFT approach. Unlike conventional schemes, our spin correction is introduced for each spin-polarized electron pair individually and therefore is expected to yield more accurate energy values. We derive an expression to extract the energy of the pure singlet state from the energy of the broken-symmetry DFT description of the low spin state and the energies of the high spin states ͑pentuplet and two spin-contaminated triplets in the case of two spin-polarized electron pairs͒. The high spin states are build with canonical natural orbitals and do not require SCF convergence.

The computational description of the catalytic processes on the surface of transition metals (TMs... more The computational description of the catalytic processes on the surface of transition metals (TMs) requires methods capable of accurate prediction of the bond forming and breaking between the atoms of metal and other elements. In our previous report [Goel and Masunov, J Chem Phys, 129, 214302, 2008], we studied TM hydrides and found that Boese-Martin functional for kinetics (BMK) combined with broken symmetry approach described dissociation process more accurately than multireference wavefunction theory (WFT) methods and some other functionals. Here, we investigate the binding energy, geometry, electronic structure, and potential energy curves for diatomic TM carbides using several exchange-correlation functionals. The functionals that include explicit dependence on the kinetic energy density (s-functionals) are considered, among others. We have found M05-2x performance to be the best, followed by BMK, when compared with experimental and high level WFT energetics. This agreement deteriorates quickly for other functionals when the fraction of the Hartree-Fock exchange is decreased. Scalar relativistic corrections yield mixed results for bond lengths and bond energies. The natural bond orbital analysis provides useful insight in description of stable spin state over others in these diatomics.