From Molecular Phylogenetics to Quantum Chemistry: Discovering Enzyme Design Principles through Computation.
Ontology highlight
ABSTRACT:
SUBMITTER: Wymore T
PROVIDER: S-EPMC3962182 | biostudies-literature | 2012
REPOSITORIES: biostudies-literature
Publications
From Molecular Phylogenetics to Quantum Chemistry: Discovering Enzyme Design Principles through Computation.
Wymore Troy T Brooks Charles L CL
Computational and structural biotechnology journal 20121130
Similar Datasets
Project description:Generative molecular design strategies have emerged as promising alternatives to trial-and-error approaches for exploring and optimizing within large chemical spaces. To date, generative models with reinforcement learning approaches have frequently used low-cost methods to evaluate the quality of the generated molecules, enabling many loops through the generative model. However, for functional molecular materials tasks, such low-cost methods are either not available or would require the generation of large amounts of training data to train surrogate machine learning models. In this work, we develop a framework that connects the REINVENT reinforcement learning framework with excited state quantum chemistry calculations to discover molecules with specified molecular excited state energy levels, specifically molecules with excited state landscapes that would serve as promising singlet fission or triplet-triplet annihilation materials. We employ a two-step curriculum strategy to first find a set of diverse promising molecules, then demonstrate the framework's ability to exploit a more focused chemical space with anthracene derivatives. Under this protocol, we show that the framework can find desired molecules and improve Pareto fronts for targeted properties versus synthesizability. Moreover, we are able to find several different design principles used by chemists for the design of singlet fission and triplet-triplet annihilation molecules.
| S-EPMC10583709 | biostudies-literature
Project description:Thermodynamics dictates the structure and function of metabolism. Redox reactions drive cellular energy and material flow. Hence, accurately quantifying the thermodynamics of redox reactions should reveal design principles that shape cellular metabolism. However, only few redox potentials have been measured, and mostly with inconsistent experimental setups. Here, we develop a quantum chemistry approach to calculate redox potentials of biochemical reactions and demonstrate our method predicts experimentally measured potentials with unparalleled accuracy. We then calculate the potentials of all redox pairs that can be generated from biochemically relevant compounds and highlight fundamental trends in redox biochemistry. We further address the question of why NAD/NADP are used as primary electron carriers, demonstrating how their physiological potential range fits the reactions of central metabolism and minimizes the concentration of reactive carbonyls. The use of quantum chemistry can revolutionize our understanding of biochemical phenomena by enabling fast and accurate calculation of thermodynamic values.
| S-EPMC6218094 | biostudies-literature
Project description:Collagen is the most abundant structural protein in humans, providing crucial mechanical properties, including high strength and toughness, in tissues. Collagen-based biomaterials are, therefore, used for tissue repair and regeneration. Utilizing collagen effectively during materials processing ex vivo and subsequent function in vivo requires stability over wide temperature ranges to avoid denaturation and loss of structure, measured as melting temperature (Tm). Although significant research has been conducted on understanding how collagen primary amino acid sequences correspond to Tm values, a robust framework to facilitate the design of collagen sequences with specific Tm remains a challenge. Here, we develop a general model using a genetic algorithm within a deep learning framework to design collagen sequences with specific Tm values. We report 1,000 de novo collagen sequences, and we show that we can efficiently use this model to generate collagen sequences and verify their Tm values using both experimental and computational methods. We find that the model accurately predicts Tm values within a few degrees centigrade. Further, using this model, we conduct a high-throughput study to identify the most frequently occurring collagen triplets that can be directly incorporated into collagen. We further discovered that the number of hydrogen bonds within collagen calculated with molecular dynamics (MD) is directly correlated to the experimental measurement of triple-helical quality. Ultimately, we see this work as a critical step to helping researchers develop collagen sequences with specific Tm values for intended materials manufacturing methods and biomedical applications, realizing a mechanistic materials by design paradigm.
| S-EPMC9546622 | biostudies-literature
Project description:We show how to use relativistic motion to generate continuous variable Gaussian cluster states within cavity modes. Our results can be demonstrated experimentally using superconducting circuits where tuneable boundary conditions correspond to mirrors moving with velocities close to the speed of light. In particular, we propose the generation of a quadripartite square cluster state as a first example that can be readily implemented in the laboratory. Since cluster states are universal resources for universal one-way quantum computation, our results pave the way for relativistic quantum computation schemes.
| S-EPMC4748225 | biostudies-other
Project description:The main descriptors of chemical bonding such as bond order (BO) and electron density at the bond critical point, ρc, are customarily used to understand the crystal and electronic structure of materials, as well as to predict their reactivity and stability. They can be obtained in the framework of crystal chemistry and quantum chemistry approaches, which are mostly applied as alternatives to each other. This paper verifies the convergence of the two approaches by analyzing a plethora of quantum chemistry data available in the literature. The exponential correlation between the electron descriptors [BO ij and ρc(ij)] and the length of chemical bonds, Rij , which is basic in crystal chemistry, was confirmed for 72 atom pairs, regardless of the nature of their interactions (ionic/covalent, metal-metal, etc.). The difference between the BO ij (Rij ) correlations obtained in this work and those accepted in crystal chemistry for the same atomic pairs does not exceed the dispersion of quantum chemistry data, confirming the qualitative validity of the BO conservation principle. Various examples are presented to show that knowledge of the exponential parameters ensures a surprisingly simple determination of two basic electron descriptors in any complex compound with known interatomic distances. In particular, the BO analysis for 20 Re6-cluster complexes illustrates the BO conservation for systems with delocalized electrons. Despite the significant transfer of electron density from the Re-Re to the Re-ligand bonds, the total number of Re valence electrons used in bonding remains close to the formal value of seven electrons.
| S-EPMC6126658 | biostudies-literature
Project description:Decoherence and gate errors severely limit the capabilities of state-of-the-art quantum computers. This work introduces a strategy for reference-state error mitigation (REM) of quantum chemistry that can be straightforwardly implemented on current and near-term devices. REM can be applied alongside existing mitigation procedures, while requiring minimal postprocessing and only one or no additional measurements. The approach is agnostic to the underlying quantum mechanical ansatz and is designed for the variational quantum eigensolver. Up to two orders-of-magnitude improvement in the computational accuracy of ground state energies of small molecules (H2, HeH+, and LiH) is demonstrated on superconducting quantum hardware. Simulations of noisy circuits with a depth exceeding 1000 two-qubit gates are used to demonstrate the scalability of the method.
| S-EPMC9933421 | biostudies-literature
Project description:Superconducting circuits offer tremendous design flexibility in the quantum regime culminating most recently in the demonstration of few qubit systems supposedly approaching the threshold for fault-tolerant quantum information processing. Competition in the solid-state comes from semiconductor qubits, where nature has bestowed some very useful properties which can be utilized for spin qubit-based quantum computing. Here we begin to explore how selective design principles deduced from spin-based systems could be used to advance superconducting qubit science. We take an initial step along this path proposing an encoded qubit approach realizable with state-of-the-art tunable Josephson junction qubits. Our results show that this design philosophy holds promise, enables microwave-free control, and offers a pathway to future qubit designs with new capabilities such as with higher fidelity or, perhaps, operation at higher temperature. The approach is also especially suited to qubits on the basis of variable super-semi junctions.
| S-EPMC4800439 | biostudies-other
Project description:We present a composite procedure for the quantum-chemical computation of spin-spin-coupled 1 H NMR spectra for general, flexible molecules in solution that is based on four main steps, namely conformer/rotamer ensemble (CRE) generation by the fast tight-binding method GFN-xTB and a newly developed search algorithm, computation of the relative free energies and NMR parameters, and solving the spin Hamiltonian. In this way the NMR-specific nuclear permutation problem is solved, and the correct spin symmetries are obtained. Energies, shielding constants, and spin-spin couplings are computed at state-of-the-art DFT levels with continuum solvation. A few (in)organic and transition-metal complexes are presented, and very good, unprecedented agreement between the theoretical and experimental spectra was achieved. The approach is routinely applicable to systems with up to 100-150 atoms and may open new avenues for the detailed (conformational) structure elucidation of, for example, natural products or drug molecules.
| S-EPMC5698732 | biostudies-literature
Project description:The properties of a polymer are known to be intrinsically related to its molecular weight distribution (MWD); however, previous methodologies of MWD control do not use a design and result in arbitrary shaped MWDs. Here we report a precise design to synthesis protocol for producing a targeted MWD design with a simple to use, and chemistry agnostic computer-controlled tubular flow reactor. To support the development of this protocol, we constructed general reactor design rules by combining fluid mechanical principles, polymerization kinetics, and experiments. The ring opening polymerization of lactide, the anionic polymerization of styrene, and the ring opening metathesis polymerization are used as model polymerizations to develop the reactor design rules and synthesize MWD profiles. The derivation of a mathematical model enables the quantitative prediction of the experimental results, and this model provides a tool to explore the limits of any MWD design protocol.
| S-EPMC7303143 | biostudies-literature
Project description:A new concept of the molecular structure optimization method based on quantum dynamics computations is presented. Nuclei are treated as quantum mechanical particles, as are electrons, and the many-body wave function of the system is optimized by the imaginary time evolution method. The numerical demonstrations with a two-dimensional H2 + system and a H-C-N system exemplify two possible advantages of our proposed method: (1) the optimized nuclear positions can be specified with a small number of observations (quantum measurements) and (2) the global minimum structure of nuclei can be obtained without starting from any sophisticated initial structure and getting stuck in the local minima. This method is considered to be suitable for quantum computers, the development of which will realize its application as a powerful method.
| S-EPMC9202041 | biostudies-literature