Utilization of formic acid by extremely thermoacidophilic archaea species.

The exploration of novel hosts with the ability to assimilate formic acid, a C1 substrate that can be produced from renewable electrons and CO, is of great relevance for developing novel and sustainable biomanufacturing platforms. Formatotrophs can use formic acid or formate as a carbon and/or reducing power source. Formatotrophy has typically been studied in neutrophilic microorganisms because formic acid toxicity increases in acidic environments below the pKa of 3.

Microbial production of high octane and high sensitivity olefinic ester biofuels.

Background: Advanced spark ignition engines require high performance fuels with improved resistance to autoignition. Biologically derived olefinic alcohols have arisen as promising blendstock candidates due to favorable octane numbers and synergistic blending characteristics. However, production and downstream separation of these alcohols are limited by their intrinsic toxicity and high aqueous solubility, respectively.

Machine learning for surrogate process models of bioproduction pathways.

Technoeconomic analysis and life-cycle assessment are critical to guiding and prioritizing bench-scale experiments and to evaluating economic and environmental performance of biofuel or biochemical production processes at scale. Traditionally, commercial process simulation tools have been used to develop detailed models for these purposes. However, developing and running such models can be costly and computationally intensive, which limits the degree to which they can be shared and reproduced in the broader research community.

Advanced one-pot deconstruction and valorization of lignocellulosic biomass into triacetic acid lactone using Rhodosporidium toruloides.

Background: Rhodosporidium toruloides is capable of co-utilization of complex carbon sources and robust growth from lignocellulosic hydrolysates. This oleaginous yeast is therefore an attractive host for heterologous production of valuable bioproducts at high titers from low-cost, deconstructed biomass in an economically and environmentally sustainable manner. Here we demonstrate this by engineering R.

Lepidopteran mevalonate pathway optimization in Escherichia coli efficiently produces isoprenol analogs for next-generation biofuels.

Terpenes constitute the largest class of natural products with over 55,000 compounds with versatile applications including drugs and biofuels. Introducing structural modifications to terpenes through metabolic engineering is an efficient and sustainable way to improve their properties. Here, we report the optimization of the lepidopteran mevalonate (LMVA) pathway towards the efficient production of isopentenyl pyrophosphate (IPP) analogs as terpene precursors.

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

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods.

Microbial production of advanced biofuels.

Concerns over climate change have necessitated a rethinking of our transportation infrastructure. One possible alternative to carbon-polluting fossil fuels is biofuels produced by engineered microorganisms that use a renewable carbon source. Two biofuels, ethanol and biodiesel, have made inroads in displacing petroleum-based fuels, but their uptake has been limited by the amounts that can be used in conventional engines and by their cost.

Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass.

Background: Mitigation of climate change requires that new routes for the production of fuels and chemicals be as oil-independent as possible. The microbial conversion of lignocellulosic feedstocks into terpene-based biofuels and bioproducts represents one such route. This work builds upon previous demonstrations that the single-celled carotenogenic basidiomycete, Rhodosporidium toruloides, is a promising host for the production of terpenes from lignocellulosic hydrolysates.

Conversion of poplar biomass into high-energy density tricyclic sesquiterpene jet fuel blendstocks.

Background: In an effort to ensure future energy security, reduce greenhouse gas emissions and create domestic jobs, the US has invested in technologies to develop sustainable biofuels and bioproducts from renewable carbon sources such as lignocellulosic biomass. Bio-derived jet fuel is of particular interest as aviation is less amenable to electrification compared to other modes of transportation and synthetic biology provides the ability to tailor fuel properties to enhance performance. Specific energy and energy density are important properties in determining the attractiveness of potential bio-derived jet fuels.

Production of ent-kaurene from lignocellulosic hydrolysate in Rhodosporidium toruloides.

Background: Rhodosporidium toruloides has emerged as a promising host for the production of bioproducts from lignocellulose, in part due to its ability to grow on lignocellulosic feedstocks, tolerate growth inhibitors, and co-utilize sugars and lignin-derived monomers. Ent-kaurene derivatives have a diverse range of potential applications from therapeutics to novel resin-based materials.

Results: The Design, Build, Test, and Learn (DBTL) approach was employed to engineer production of the non-native diterpene ent-kaurene in R.

Small Current but Highly Productive Synthesis of 1,3-Propanediol from Glycerol by an Electrode-Driven Metabolic Shift in Klebsiella pneumoniae L17.

Electrofermentation actively regulates the bacterial redox state, which is essential for bioconversion and has been highlighted as an effective method for further improvements of the productivity of either reduced or oxidized platform chemicals. 1,3-Propanediol (1,3-PDO) is an industrial value-added chemical that can be produced from glycerol fermentation. The bioconversion of 1,3-PDO from glycerol requires additional reducing energy under anoxic conditions.

Monoterpene production by the carotenogenic yeast Rhodosporidium toruloides.

Background: Due to their high energy density and compatible physical properties, several monoterpenes have been investigated as potential renewable transportation fuels, either as blendstocks with petroleum or as drop-in replacements for use in vehicles (both heavy and light-weight) or in aviation. Sustainable microbial production of these biofuels requires the ability to utilize cheap and readily available feedstocks such as lignocellulosic biomass, which can be depolymerized into fermentable carbon sources such as glucose and xylose. However, common microbial production platforms such as the yeast Saccharomyces cerevisiae are not naturally capable of utilizing xylose, hence requiring extensive strain engineering and optimization to efficiently utilize lignocellulosic feedstocks.

Short-chain ketone production by engineered polyketide synthases in Streptomyces albus.

Microbial production of fuels and commodity chemicals has been performed primarily using natural or slightly modified enzymes, which inherently limits the types of molecules that can be produced. Type I modular polyketide synthases (PKSs) are multi-domain enzymes that can produce unique and diverse molecular structures by combining particular types of catalytic domains in a specific order. This catalytic mechanism offers a wealth of engineering opportunities.

a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts.

Background: Economical conversion of lignocellulosic biomass into biofuels and bioproducts is central to the establishment of a robust bioeconomy. This requires a conversion host that is able to both efficiently assimilate the major lignocellulose-derived carbon sources and divert their metabolites toward specific bioproducts.

Results: In this study, the carotenogenic yeast was examined for its ability to convert lignocellulose into two non-native sesquiterpenes with biofuel (bisabolene) and pharmaceutical (amorphadiene) applications.

Optimization of Methanotrophic Growth and Production of Poly(3-Hydroxybutyrate) in a High-Throughput Microbioreactor System.

Production of poly(3-hydroxybutyrate) (P3HB) from methane has economic and environmental advantages over production by agricultural feedstock. Identification of high-productivity strains and optimal growth conditions is critical to efficient conversion of methane to polymer. Current culture conditions, including serum bottles, shake flasks, and agar plates, are labor-intensive and therefore insufficient for systematic screening and isolation.

A simple way to test for collinearity in spin symmetry broken wave functions: general theory and application to generalized Hartree Fock.

We introduce a necessary and sufficient condition for an arbitrary wavefunction to be collinear, i.e., its spin is quantized along some axis.

Restricted Hartree Fock using complex-valued orbitals: a long-known but neglected tool in electronic structure theory.

Restricted Hartree Fock using complex-valued orbitals (cRHF) is studied. We introduce an orbital pairing theorem, with which we obtain a concise connection between cRHF and real-valued RHF, and use it to uncover the close relationship between cRHF, unrestricted Hartree Fock, and generalized valence bond perfect pairing. This enables an intuition for cRHF, contrasting with the generally unintuitive nature of complex orbitals.

Spin-flip non-orthogonal configuration interaction: a variational and almost black-box method for describing strongly correlated molecules.

In this paper, we report the development, implementation, and assessment of a novel method for describing strongly correlated systems, spin-flip non-orthogonal configuration interaction (SF-NOCI). The wavefunction is defined to be a linear combination of independently relaxed Slater determinants obtained from all possible spin-flipping excitations within a localized orbital active-space, typically taken to be the singly occupied orbitals of a high-spin ROHF wavefunction. The constrained orbital optimization of each CI basis configuration is defined such that only non-active-space orbitals are allowed to relax (all active space orbitals are fixed).

Disassembly and reassembly of polyhydroxyalkanoates: recycling through abiotic depolymerization and biotic repolymerization.

An abiotic-biotic strategy for recycling of polyhydroxyalkanoates (PHAs) is evaluated. Base-catalyzed PHA depolymerization yields hydroxyacids, such as 3-hydroxybutyrate (3HB), and alkenoates, such as crotonate; catalytic thermal depolymerization yields alkenoates. Cyclic pulse addition of 3HB to triplicate bioreactors selected for an enrichment of Comamonas, Brachymonas and Acinetobacter.

Complex absorbing potentials within EOM-CC family of methods: theory, implementation, and benchmarks.

A production-level implementation of equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) for electron attachment and excitation energies augmented by a complex absorbing potential (CAP) is presented. The new method enables the treatment of metastable states within the EOM-CC formalism in a similar manner as bound states. The numeric performance of the method and the sensitivity of resonance positions and lifetimes to the CAP parameters and the choice of one-electron basis set are investigated.

Non-orthogonal configuration interaction for the calculation of multielectron excited states.

We apply Non-orthogonal Configuration Interaction (NOCI) to molecular systems where multielectron excitations, in this case double excitations, play a substantial role: the linear polyenes and β-carotene. We demonstrate that NOCI when applied to systems with extended conjugation, provides a qualitatively correct wavefunction at a fraction of the cost of many other multireference treatments. We also present a new extension to this method allowing for purification of higher-order spin states by utilizing Generalized Hartree-Fock Slater determinants and the details for computing ⟨S(2)⟩ for the ground and excited states.

Unrestricted absolutely localized molecular orbitals for energy decomposition analysis: theory and applications to intermolecular interactions involving radicals.

Radical-closed shell and radical-radical intermolecular interactions are less well-understood than those between closed shell species. With the objective of gaining additional insight, this work reports a generalization of the absolutely localized molecular orbital (ALMO) energy decomposition analysis (EDA) to open shell fragments, described by self-consistent field methods, such as standard density functional theory. The ALMO-EDA variationally partitions an intermolecular interaction energy into three separate contributions; frozen orbital interactions, polarization, and charge transfer.

Useful lower limits to polarization contributions to intermolecular interactions using a minimal basis of localized orthogonal orbitals: theory and analysis of the water dimer.

The problem of describing the energy-lowering associated with polarization of interacting molecules is considered in the overlapping regime for self-consistent field wavefunctions. The existing approach of solving for absolutely localized molecular orbital (ALMO) coefficients that are block-diagonal in the fragments is shown based on formal grounds and practical calculations to often overestimate the strength of polarization effects. A new approach using a minimal basis of polarized orthogonal local MOs (polMOs) is developed as an alternative.