Geoffrey R Hutchison

• Ph.D., Chemistry
• Professor (Assistant) at University of Pittsburgh

Interoperability in computational chemistry is elusive, impeded by the independent development of software packages and idiosyncratic nature of their output files. The cclib library was introduced in 2006 as an attempt to improve this situation by providing a consistent interface to the results of various quantum chemistry programs. The shared API...

Accurate prediction of micro-pKa values is crucial for understanding and modulating the acidity and basicity of organic molecules, with applications in drug discovery, materials science, and environmental chemistry. This work introduces QupKake, a novel method that combines graph neural network models with semiempirical quantum mechanical (QM) feat...

The design of high-performing OSC materials is an active field of research. Many review articles summarize certain subclasses of NFAs, however, no broad overall analysis has been performed on the photovoltaic impact of chemical modifications made. This meta-analysis investigates various molecular design strategies for NFAs and donors and their effe...

We performed exhaustive torsion sampling on more than 3 million compounds using the GFN2-xTB method and performed a comparison of experimental crystallographic and gas-phase conformers. Many conformer sampling methods derive torsional angle distributions from experimental crystallographic data, limiting the torsion preferences to molecules that mus...

We have performed exhaustive torsion sampling on more than 3 million compounds using the GFN2 method and performed a comparison of experimental crystallographic and gas-phase conformers. Many conformer sampling methods derive torsional angle distributions from experimental crystallographic data, limiting the torsion preferences to molecules that mu...

Conformer generation, the assignment of realistic 3D coordinates to a small molecule, is fundamental to structure-based drug design. Conformational ensembles are required for rigid-body matching algorithms, such as shape-based or pharmacophore approaches, and even methods that treat the ligand flexibly, such as docking, are dependent on the quality...

Genetic algorithms (GAs) are a powerful tool to search large chemical spaces for inverse molecular design. However, GAs have multiple hyperparameters that have not been thoroughly investigated for chemical space searches. In this tutorial, we examine the general effects of a number of hyperparameters, such as population size, elitism rate, selectio...

We have performed exhaustive torsion sampling on more than 3 million compounds using the GFN2 method and performed a comparison of experimental crystallographic and gas-phase conformers. Many conformer sampling methods derive torsional angle distributions from experimental crystallographic data, limiting the torsion preferences to molecules that mu...

Genetic algorithms (GAs) are a powerful tool to search large chemical spaces for inverse molecular design. However, GAs have multiple hyperparameters that have not been thoroughly investigated for chemical space searches. In this work, we examine the general effects of a number of hyperparameters, such as population size, elitism rate, selection me...

Conformer generation, the assignment of realistic 3D coordinates to a small molecule, is fundamental to structure based drug design. Conformational ensembles are required for rigid-body matching algorithms, such as shape-based or pharmacophore approaches, and even methods that treat the ligand flexibly, such as docking, are dependent on the quality...

We have performed exhaustive torsion sampling on more than 3 million compounds using the GFN2 method and performed a comparison of experimental crystallographic and gas-phase conformers. Many conformer sampling methods derive torsional angle distributions from experimental crystallographic data, limiting the torsion preferences to molecules that mu...

Stable ground-state triplet π-conjugated copolymers have many interesting electronic and optoelectronic properties. However, the large number of potential monomer combinations makes it impractical to synthesize or even just use density functional theory (DFT) to calculate their triplet ground-state stability. Here, we present a genetic algorithm im...

In the design of organic solar cells, there has been a need for materials with high power conversion efficiencies. Scharber's model is commonly used to predict efficiency; however, it exhibits poor performance with new non-fullerene acceptor (NFA) devices, since it was designed for fullerene-based devices. In this work, an empirical model is propos...

Given the importance of accurate polarizability calculations to many chemical applications, coupled with the need for efficiency when calculating the properties of sets of molecules or large oligomers, we present a benchmark study examining possible calculation methods for polarizable materials. We first investigate the accuracy of highly-efficient...

Given the importance of accurate polarizability calculations to many chemical applications, coupled with the need for efficiency when calculating the properties of sets of molecules or large oligomers, we present a benchmark study examining possible calculation methods for polarizable materials. We first investigate the accuracy of highly-efficient...

Organic π-conjugated polymers with a triplet ground state have been the focus of recent research for their interesting and unique electronic properties, arising from the presence of the two unpaired electrons. These polymers are usually built from alternating electron-donating and electron-accepting monomer pairs which lower the HOMO-LUMO gap and y...

Given the importance of accurate polarizability calculations to many chemical applications, coupled with the need for efficiency when calculating the properties of sets of molecules or large oligomers, we present a benchmark study examining possible calculation methods for polarizable materials. We first investigate the accuracy of highly-efficient...

Given the importance of accurate polarizability calculations to many chemical applications, coupled with the need for efficiency when calculating the properties of sets of molecules or large oligomers, we present a benchmark study examining possible calculation methods for polarizable materials. We first investigate the accuracy of highly-efficient...

Computing quantum chemical properties of small molecules and polymers can provide insights valuable into physicists, chemists, and biologists when designing new materials, catalysts, biological probes, and drugs. Deep learning can compute quantum chemical properties accurately in a fraction of time required by commonly used methods such as density...

Understanding and predicting the charge transport properties of π-conjugated materials is an important challenge for designing new organic electronic applications, including solar cells, plastic transistors, light-emitting devices, and chemical sensors. A key component of the hopping mechanism of charge transfer in these materials is the Marcus reo...

The calculation of the entropy of flexible molecules can be challenging, since the number of possible conformers can grow exponentially with molecule size and many low-energy conformers may be thermally accessible. Different methods have been proposed to approximate the contribution of conformational entropy to the molecular standard entropy, inclu...

While many machine learning (ML) methods, particularly deep neural networks, have been trained for density functional and quantum chemical energies and properties, the vast majority of these methods focus on single-point energies. In principle, such ML methods, once trained, offer thermochemical accuracy on par with density functional and wave func...

The geometry of a molecule plays a significant role in determining its physical and chemical properties. Despite its importance, there are relatively few studies on ring puckering and conformations, often focused on small cycloalkanes, 5- and 6-membered carbohydrate rings, and specific macrocycle families. We lack a general understanding of the puc...

div>The geometry of a molecule plays a significant role in determining its physical and chemical properties. Despite its importance, there are relatively few studies on ring puckering and conformations, often focused on small cycloalkanes, five- and six-membered carbohydrate rings and specific macrocycle families. We lack a general understanding of...

The calculation of the entropy of flexible molecules can be challenging, since the number of possible conformers grows exponentially with molecule size and many low-energy conformers may be thermally accessible. Different methods have been proposed to approximate the contribution of conformational entropy to the molecular standard entropy, includin...

We have performed a large-scale evaluation of current computational methods, including conventional small-molecule force fields, semiempirical, density functional, ab initio electronic structure methods, and current machine learning (ML) techniques to evaluate relative single-point energies. Using up to 10 local minima geometries across ~700 molecu...

In response to an applied electric field, materials and even individual molecules can exhibit electromechanical response. Previous work has demonstrated the piezoelectric distortion of polar organic crystals, biomaterials, and even single molecular monolayers, increasing length in response to the change in potential energy of interaction between th...

Hydrogen bonds, ubiquitous in organic and biological materials, involve weak electrostatic interactions, which can geometrically distort in response to an applied electric field. This electromechanical response is a key component in a range of piezoelectric materials in applications including energy harvesting and sensing. In this work, we apply el...

div>A key challenge in conformer sampling is to find low-energy conformations with a small number of energy evaluations. We have recently demonstrated Bayesian optimization as an effective method to search for energetically favorable conformations. This approach balances between exploitation and exploration , and lead to superior performance when c...

Rapidly predicting an accurate three dimensional geometry of a molecule is a crucial task for cheminformatics and across a wide range of molecular modeling. Consequently, developing a fast, accurate, and open implementation of structure prediction is necessary for reproducible cheminformatics research. We introduce a fragment-based coordinate gener...

While photopatterning is in widespread use for patterning inorganic semiconductors, patterning of widely-used gold-thiol organic self-assembled monolayers is typically done with contact methods. Through common atomic force microscope techniques and quantification of the energy impinging on the target surface, the energy required for UV-photooxidati...

We report a new methodology for the electromechanical characterization of organic monolayers based on the implementation of dual AC resonance tracking piezo force microscopy (DART-PFM) combined with a sweep of an applied DC field under a fixed AC field. This experimental design allows calibration of the electrostatic component of the tip response a...

Generating low-energy molecular conformers is a key task for many areas of computational chemistry, molecular modeling and cheminformatics. Most current conformer generation methods primarily focus on generating geometrically diverse conformers rather than finding the most probable or energetically lowest minima. Here, we present a new stochastic s...

This work illustrates some of the shortcomings of the standard donor-acceptor model as a tool for predicting polymer molecular orbital interactions. 8741 DFT calculations were performed for a series of co-oligomers of varying length from a diverse set of 91 thiophene monomers to explore statistical relationships between the frontier molecular orbit...

div>Rapidly predicting an accurate three dimensional geometry of a molecule is a crucial task in cheminformatics and a range of molecular modeling. Fast, accurate, and open implementation of structure prediction is necessary for reproducible cheminformatics research. We introduce fragment-based coordinate generation for Open Babel, a widely accepte...

Despite considerable research interest in developing new piezoelectric materials, little work has focused on the fundamental design of these materials from the ground up. Herein, we present a general, versatile method for producing tunable, flexible piezoelectric energy harvesters (PEHs) with excellent piezoelectric response. Using a poly(dimethyls...

div> Generating low-energy molecular conformers is a key task for many areas of computational chemistry, molecular modeling and cheminformatics. Most current conformer generation methods primarily focus on generating geometrically diverse conformers rather than finding the most probable or energetically lowest minima. Here, we present a new stocha...

Gas phase electric properties of molecules can be computed routinely using wave function methods or the density functional theory (DFT). However, these methods remain computationally expensive for high-throughput screening of the vast chemical space of virtual compounds. Therefore, empirical force fields are a more practical choice in many cases, p...

Submitted manuscript that describes derivation of atomic polarization and exponents for Gaussian or Slater distribution functions to describe polarizable atoms in force fields. Parameters are provided based on the General Amber Force Field, for H, C, N, O, F, P, S, Cl, Br, I.<br

Many biomaterials are piezoelectric (i.e., mechanically deform under an applied electric field); however, the molecular origin of this phenomenon remains unclear. In the case of protein-based scaffolds, one possibility involves flexible response of local folding motifs to the applied field. Here, we test this hypothesis by examining piezo response...

We have carried out a large scale computational investigation to assess the utility of common small-molecule force fields for computational screening of low energy conformers of typical organic molecules. Using statistical analyses on the energies and relative rankings of up to 250 diverse conformers of 700 different molecular structures, we find t...

Developing a bottom-up (molecular) theory for the electromechanical response of aperiodic materials is a prerequisite for understanding the piezoelectric properties of systems such as nanoparticles, (non-crystalline) polymers, or biomolecule agglomerates. The focus of this publication is to establish a new language and formalism for describing mole...

Conjugated organic molecules represent an important area of materials chemistry for both fundamental scientific exploration and technological applications. Using a genetic algorithm to computationally screen up to ~25-50 million molecules for organic photovoltaic properties, we find that our methods find top monomers 6,000-8,000 times faster than b...

Using a diverse set of 100 oligothiophenes, extrapolated oligomer and polymer HOMO, LUMO and HOMO-LUMO gaps are shown to be accurately estimated from the computed values of the trimer HOMO, trimer LUMO and trimer HOMO-LUMO gaps. These simple approximations can be improved further through easy to calculate properties of monomers or small oligomers....

We demonstrate that an applied electric field causes piezoelectric distortion across single molecular monolayers of oligopeptides. We deposited self-assembled monolayers ~1.5 nm high onto smooth gold surfaces. These monolayers exhibit strong piezoelectric response that varies linearly with applied bias (1-3V), measured using piezoresponse force mic...

Ferroelectric materials can switch their polarization in response to an applied electric field. In this work, ferroelectricity at the single molecule level is proposed and investigated using density functional theory (DFT) calculations. Several bowl-shaped molecules, both synthetically reported and hypothetically proposed, are shown to invert polar...

We have carried out a large scale computational investigation to assess the utility of common classical force fields for computational screening of low energy conformers. Using statistical analyses on the energies and relative rankings of up to 250 diverse conformers of 700 different molecular structures, we find that energies from widely-used clas...

To understand the influence of monomer sequence on the properties and performance of conjugated oligomers, a series of dimers, trimers, and tetramers were prepared from phenylene (P) and benzothiadiazole (B) monomers linked by vinylene groups. Optical and electro-chemical studies established the influence of sequence on both the A,a), and redox pot...

To investigate the sequence effect on donor-acceptor conjugated oligomers and polymers, the trimeric isomers PBP and BPP, comprising dialkoxy phenylene vinylene (P), benzothiadiazole vinylene (B), and alkyl endgroups with terminal olefins, are synthesized. Sequence effects are evident in the optical/electrochemical properties and thermal properties...

We report flexible piezoelectric polyurethane foams with d33 piezocoefficients up to 244 ± 30 pC N-1. Polymer foams have large volume changes under applied force, and dipole-doped polymers can have large polarizations even when poled at fields two orders of magnitude lower than space-charge electrets. Combining these features results in piezocoeffi...

This is an archive of the source code for cclib version 1.5, orginally released on github (https://github.com/cclib/cclib/releases/tag/v1.5).

Monte Carlo simulations of charge transport in organic solar cells are performed for ideal and isotropic bulk heterojunction morphologies while altering the delocalization length of charge carriers. Previous device simulations have either treated carriers as point charges or with a highly delocalized mean-field treatment. This new model of charge d...

Conjugated organic polymers offer a highly tailorable set of optical and electronic properties and show promise for a wide range of technological applications including light-emitting devices and solar cells. A key challenge is to tune the HOMO and LUMO energies and the HOMO-LUMO gap for particular applications. Sequence control of monomer order of...

Organic piezoelectric materials are promising targets in applications such as energy harvesting or mechanical sensors and actuators. In a recent paper we have shown that hydrogen bonding gives rise to a significant piezoelectric response. In this paper, we aim to find organic hydrogen bonded systems with increased piezo-response by investigating di...

Organic electronic devices promise cheaper solution processability than their inorganic counterparts and allow for the vast tailorability of synthetic chemistry to tune properties and efficiency. A critical fundamental challenge is to understand the dynamics and mechanisms of charge transport, particularly the role of defects and traps. We use Kelv...

Conventional piezoelectric materials change shape in response to an applied external electric field, frequently deforming at grain boundaries in addition to intrinsic unit cell changes. We detail a computational investigation, using density functional theory (DFT) calculations of single-molecule piezoelectrics. Rather than deforming along covalent...

The piezoelectric properties of 2-methyl-4-nitroaniline crystals were explored qualitatively and quantitatively using an electrostatically embedded many-body (EE-MB) expansion scheme for the correlation energies of a system of monomers within the crystal. The results demonstrate that hydrogen bonding is an inherently piezoelectric interaction, defo...

There has been increasing interest in rational, computationally driven design methods for materials, including organic photovoltaics (OPVs). Our approach focuses on a screening “pipeline”, using a genetic algorithm for first stage screening and multiple filtering stages for further refinement. An important step forward is to expand our diversity of...

Although sequence must necessarily affect the photophysical properties of oligomers and copolymers prepared from donor and acceptor monomers, little is known about this effect, as nearly all the donor/acceptor materials have an alternating structure. A series of sequenced p-phenylene–vinylene (PV) oligomers was synthesized and investigated both exp...

The effect of morphology on charge transport in organic photovoltaics is assessed using Monte Carlo. In isotopic two-phase morphologies, increasing the domain size from 6.3 to 18.3 nm improves the fill factor by 11.6%, a result of decreased tortuosity and relaxation of Coulombic barriers. Additionally, when small aggregates of electron acceptors ar...

Here, we report an unusual oxidation-induced photoluminescence (PL) turn-on response of a poly(3-alkoxythiophene), poly(3-{2-[2-(2-ethoxyethoxy)ethoxy]ethoxy}thiophene) (PEEEET). PEEEET shows a significantly red-shifted absorption spectrum compared to polyalkylthiophenes and is almost non-fluorescent (quantum yield < 1%) in its pristine state. The...

Electron delocalization of new mixed-valent (MV) systems with the aid of lateral metal chelation is reported. 2,2'-Bipyridine (bpy) derivatives with one or two appended di-p-anisylamino groups on the 5,5'-positions and a coordinated [Ru(bpy)(2) ] (bpy=2,2'-bipyridine), [Re(CO)(3) Cl], or [Ir(ppy)(2) ] (ppy=2-phenylpyridine) component were prepared....

Monte Carlo simulations were used to investigate the carrier dynamics in realistic, finite-sized, small-molecule, organic field-effect transistors (OFETs) within the first few nanoseconds of device turn-on as well as when the system equilibrates. The results show that the device current exhibits large magnitude oscillations (64 +/- 27 nA) during de...

Background The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structu...

Monte Carlo simulations were used to study the effects of explicit charge traps on charge transport in small-molecule organic field effect transistors. The results show that the source-drain current decreases as the trap/barrier concentration increases, reaches a minimum around 30/70%, and increases as the concentration reaches 100%, regardless of...

ABSTRACT: The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community...

ABSTRACT: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitud...

Standard and constrained density functional theory calculations were used to study the degree of charge localization in positively charged bithiophene clusters. Although polarization effects due to the crystalline environment are known, many charge-transport models in π-conjugated organic materials assume a highly localized picture of carriers due...

Conjugated organic polymers are key building blocks of low-cost photovoltaic materials. We have examined over 90 000 copolymers using computational predictions to solve the “inverse design” of molecular structures with optimum properties for highly efficient solar cells (specifically matching optical excitation energies and excited-state energies)....

Background Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-energy conformers according to a diversity criterion. Results Confab generates conformations using the 'torsion driving approach' w...

The area of organic photovoltaic materials has elicited great interest in both the scientific and technological communities due to its potential to deliver cheap and highly efficient solar cells [1]. To date, however, such so-called molecular wires have typically yielded energy conversion efficiencies of only ~5-6% despite a theoretical maximum of...

Crystal structures used to test conformational coverage. This is a text file in SDF format containing biological conformations (as downloaded from PubChem) of 1000 molecules. This is a subset of the data used in the study by Borodina et al.

Generated 3D structures used to test conformational coverage. This is a text file in SDF format containing 3D structures of the 1000 molecules in the dataset generated using Open Babel. These were used as the input to Confab.

Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-energy conformers according to a diversity criterion. Confab generates conformations using the 'torsion driving approach' which involves iterati...

The effects of defects and electrostatics on charge transport in realistic organic field effect transistors were studied using a combination of first principles quantum chemistry calculations and Monte Carlo simulations with explicit introduction of defect sites. The results show that electrostatic interactions dramatically affect the field and car...

Understanding the roles of charge traps and defects in electronic transport in organic materials is becoming increasingly important. Computational studies have been undertaken, using an agent-based Monte Carlo method, of the active region of a monolayer FET. Charge transport is assumed to be due to thermally activated, variable-range hopping betwee...

With the rising interest in organic electronic materials, an understanding of electronic transport, and the effects of defects on electronic transport, will be an important step towards a useful understanding of these materials. To this end, 2,2':6',2'' terpyridine will be used to make metal complexes which can act as organic semiconductors. Contro...

We are building up experimental and computational model systems for charge transport in nanoscale organic electronic devices. In particular, our combined approach is aimed at addressing questions as to the effect of impurities, traps, and other defects on electronic conductivity. Experimentally, we have designed thin films and monolayers to which w...

The Avogadro project is a free, open source approach to building chemical structures. It has integrated analysis, and three-dimensional visualization capabilities. Avogadro also uses external packages to perform quantum structure calculations. The work presented here illustrates a novel approach to working with the results of quantum calculations b...

Open Source cheminformatics toolkits such as OpenBabel, the CDK and the RDKit share the same core functionality but support different sets of file formats and forcefields, and calculate different fingerprints and descriptors. Despite their complementary features, using these toolkits in the same program is difficult as they are implemented in diffe...

Timing Code. A zip file containing Python, Java and C++ code used for run time comparisons for two test cases.

Miniwebsite Depictions. A mini-website showing a comparison of the depictions generated by several cheminformatics toolkits.

Pybel API. The HTML documentation of the Pybel API (application programming interface).

We present a study of the electrochemical properties of a set of oligothiophenes including 2,5-bis(methylthio)thiophene (BMTT), its derivatives, and 5,5‘-bis(methylthio)-2,2‘-bithiophene (BMTbT). BMTbT, which possesses an α-coupled bithiophene capped with methylthio groups, exhibited two one-electron reversible processes at 3.8 and 4.0 V vs Li/Li+,...

Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that pro...

We present a family of a novel class of organosulfur compounds based on dimercaptothiophene and its derivatives, with a variety of functional groups ( electron- donating or electron- withdrawing groups) and regiochemistries, designed as potential high- energy cathode materials with sufficient charge/ discharge cyclability for lithium/ lithium- ion...

We illustrate our current work for electrochemical energy generation and storage (i.e., fuel cells and lithium-ion batteries, respectively). In fuel cell research, we have been developing Pt-based ordered intermetallic compounds as electrocatalysts towards anodic reactions of liquid fuels such as methanol, ethanol, and formic acid for proton-exchan...

We study electron transport through C(60) molecules in the Kondo regime using a mechanically controllable break junction. By varying the electrode spacing, we are able to change both the width and the height of the Kondo resonance, indicating modification of the Kondo temperature and the relative strength of coupling to the two electrodes. The line...

The Blue Obelisk Movement (http://www.blueobelisk.org/) is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards. We outline recent examples of cooperation in the Blue Obelisk group: a shared dictionary of alg...