Artículos de revistas: "Quantum Chemical Computation"

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Huggins, William J., Bryan A. O’Gorman, Nicholas C. Rubin, David R. Reichman, Ryan Babbush y Joonho Lee. "Unbiasing fermionic quantum Monte Carlo with a quantum computer". Nature 603, n.º 7901 (16 de marzo de 2022): 416–20. http://dx.doi.org/10.1038/s41586-021-04351-z.

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AbstractInteracting many-electron problems pose some of the greatest computational challenges in science, with essential applications across many fields. The solutions to these problems will offer accurate predictions of chemical reactivity and kinetics, and other properties of quantum systems1–4. Fermionic quantum Monte Carlo (QMC) methods5,6, which use a statistical sampling of the ground state, are among the most powerful approaches to these problems. Controlling the fermionic sign problem with constraints ensures the efficiency of QMC at the expense of potentially significant biases owing to the limited flexibility of classical computation. Here we propose an approach that combines constrained QMC with quantum computation to reduce such biases. We implement our scheme experimentally using up to 16 qubits to unbias constrained QMC calculations performed on chemical systems with as many as 120 orbitals. These experiments represent the largest chemistry simulations performed with the help of quantum computers, while achieving accuracy that is competitive with state-of-the-art classical methods without burdensome error mitigation. Compared with the popular variational quantum eigensolver7,8, our hybrid quantum-classical computational model offers an alternative path towards achieving a practical quantum advantage for the electronic structure problem without demanding exceedingly accurate preparation and measurement of the ground-state wavefunction.

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2

Sarotti, Ariel M. "Quantum chemical computation and machine learning in NMR". Magnetic Resonance in Chemistry 58, n.º 6 (6 de abril de 2020): 477. http://dx.doi.org/10.1002/mrc.5016.

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3

CLARK, JOHN W., DENNIS G. LUCARELLI y TZYH-JONG TARN. "CONTROL OF QUANTUM SYSTEMS". International Journal of Modern Physics B 17, n.º 28 (10 de noviembre de 2003): 5397–411. http://dx.doi.org/10.1142/s021797920302051x.

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A quantum system subject to external fields is said to be controllable if these fields can be adjusted to guide the state vector to a desired destination in the state space of the system. Fundamental results on controllability are reviewed against the background of recent ideas and advances in two seemingly disparate endeavours: (i) laser control of chemical reactions and (ii) quantum computation. Using Lie-algebraic methods, sufficient conditions have been derived for global controllability on a finite-dimensional manifold of an infinite-dimensional Hilbert space, in the case that the Hamiltonian and control operators, possibly unbounded, possess a common dense domain of analytic vectors. Some simple examples are presented. A synergism between quantum control and quantum computation is creating a host of exciting new opportunities for both activities. The impact of these developments on computational many-body theory could be profound.

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4

Gaita-Ariño, A., F. Luis, S. Hill y E. Coronado. "Molecular spins for quantum computation". Nature Chemistry 11, n.º 4 (22 de marzo de 2019): 301–9. http://dx.doi.org/10.1038/s41557-019-0232-y.

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5

Li, Junxu y Sabre Kais. "Entanglement classifier in chemical reactions". Science Advances 5, n.º 8 (agosto de 2019): eaax5283. http://dx.doi.org/10.1126/sciadv.aax5283.

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The Einstein, Podolsky, and Rosen (EPR) entanglement, which features the essential difference between classical and quantum physics, has received wide theoretical and experimental attentions. Recently, the desire to understand and create quantum entanglement between particles such as spins, photons, atoms, and molecules is fueled by the development of quantum teleportation, quantum communication, quantum cryptography, and quantum computation. Although most of the work has focused on showing that entanglement violates the famous Bell’s inequality and its generalization for discrete measurements, few recent attempts focus on continuous measurement results. Here, we have developed a general practical inequality to test entanglement for continuous measurement results, particularly scattering of chemical reactions. After we explain how to implement this inequality to classify entanglement in scattering experiments, we propose a specific chemical reaction to test the violation of this inequality. The method is general and could be used to classify entanglement for continuous measurement results.

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6

Kirby, William M., Andrew Tranter y Peter J. Love. "Contextual Subspace Variational Quantum Eigensolver". Quantum 5 (14 de mayo de 2021): 456. http://dx.doi.org/10.22331/q-2021-05-14-456.

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We describe the contextual subspace variational quantum eigensolver (CS-VQE), a hybrid quantum-classical algorithm for approximating the ground state energy of a Hamiltonian. The approximation to the ground state energy is obtained as the sum of two contributions. The first contribution comes from a noncontextual approximation to the Hamiltonian, and is computed classically. The second contribution is obtained by using the variational quantum eigensolver (VQE) technique to compute a contextual correction on a quantum processor. In general the VQE computation of the contextual correction uses fewer qubits and measurements than the VQE computation of the original problem. Varying the number of qubits used for the contextual correction adjusts the quality of the approximation. We simulate CS-VQE on tapered Hamiltonians for small molecules, and find that the number of qubits required to reach chemical accuracy can be reduced by more than a factor of two. The number of terms required to compute the contextual correction can be reduced by more than a factor of ten, without the use of other measurement reduction schemes. This indicates that CS-VQE is a promising approach for eigenvalue computations on noisy intermediate-scale quantum devices.

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7

Lisnchenko, M. O. y S. I. Protasov. "Protein folding quantum circuit quantum circuit for bio material modelling compression". Izvestiya Vysshikh Uchebnykh Zavedenii. Materialy Elektronnoi Tekhniki = Materials of Electronics Engineering 25, n.º 4 (10 de enero de 2023): 305–11. http://dx.doi.org/10.17073/1609-3577-2022-4-305-311.

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Computational material science aims to simulate substances to understand their physical properties. Bioelectronics is an interdisciplinary field that studies biological material from the conductivity point of view. In case of proteins, the folding is an important feature that directly influences physical and chemical properties. The folding modelling is a hard task. The enormous number of degrees of freedom makes modelling impossible for classical computation due to resource limits. Quantum computations aim to process multidimensional data with logarithmic growth of quantum bits. Quantum operators (gates) form quantum programs, known as circuits that process the input data. In real quantum computers, the gates are noisy and expensive to execute. Thus, it is essential to reduce the number of quantum gates both for the quality of the result and the cost of computations. This work describes an approach to decrease the number of quantum gates based on their mathematical property. The matrix properties form the first optimization technique. In this case, the optimized quantum circuit predicts precisely the same protein folding as the not optimized circuit predicts. This happens because both of the circuits are mathematically equivalent. The removal of weakly-parametrized gates forms the second optimization technique. In such case the optimized quantum circuit calculates the approximate protein folding. The error depends on parameter’s amplitude of the gates. The first technique allows to decrease the circuit depth from 631 to 629 gates while modelling the part of Azurin peptide. The second technique allows to decrease the depth to 314 gates with the threshold parameter value 0.4 radians.

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8

Lloyd, Austin, Helen Moylan y Joseph McDouall. "Modelling the Effect of Zero-Field Splitting on the 1H, 13C and 29Si Chemical Shifts of Lanthanide and Actinide Compounds". Magnetochemistry 5, n.º 1 (11 de enero de 2019): 3. http://dx.doi.org/10.3390/magnetochemistry5010003.

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The prediction of paramagnetic NMR (pNMR) chemical shifts in molecules containing heavy atoms presents a significant challenge to computational quantum chemistry. The importance of meeting this challenge lies in the central role that NMR plays in the structural characterisation of chemical systems. Hence there is a need for reliable assignment and prediction of chemical shifts. In a previous study [Trends in Physical Chemistry, 17, 25–57, (2017)] we looked at the computation of pNMR chemical shifts in lanthanide and actinide complexes using a spin Hamiltonian approach. In that study we were principally concerned with molecules with S = 1/2 ground states. In the present work we extend that study by looking at the effect of zero field splitting (ZFS) for six complexes with S = 3/2 ground states. It is shown that the inclusion of ZFS can produce substantial shifts in the predicted chemical shifts. The computations presented are typically sufficient to enable assignment of experimental spectra. However for one case, in which the peaks are closely clustered, the inclusion of ZFS re-orders the chemical shifts making assignment quite difficult. We also observe, and echo, the previously reported importance of including the paramagnetic spin-orbit hyperfine interaction for 13 C and 29 Si atoms, when these are directly bound to a heavy element and thus subject to heavy-atom-light-atom effects. The necessary computations are very demanding, and more work is needed to find theoretical and computational approaches that simplify the evaluation of this term. We discuss the computation of each term required in the spin Hamiltonian. The systems we study in this work are restricted to a single heavy atom ion (one Nd(III) and five U(III) complexes), but typify some of the computational complexity encountered in lanthanide and actinide containing molecules.

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9

Alkan, Fahri y C. Dybowski. "Chemical-shift tensors of heavy nuclei in network solids: a DFT/ZORA investigation of 207Pb chemical-shift tensors using the bond-valence method". Physical Chemistry Chemical Physics 17, n.º 38 (2015): 25014–26. http://dx.doi.org/10.1039/c5cp03348a.

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Accurate computation of ²⁰⁷Pb magnetic shielding principal components is within the reach of quantum chemistry methods by employing relativistic ZORA/DFT and cluster models adapted from the bond valence model.

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10

Genoni, Alessandro. "On the use of the Obara–Saika recurrence relations for the calculation of structure factors in quantum crystallography". Acta Crystallographica Section A Foundations and Advances 76, n.º 2 (11 de febrero de 2020): 172–79. http://dx.doi.org/10.1107/s205327332000042x.

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Modern methods of quantum crystallography are techniques firmly rooted in quantum chemistry and, as in many quantum chemical strategies, electron densities are expressed as two-centre expansions that involve basis functions centred on atomic nuclei. Therefore, the computation of the necessary structure factors requires the evaluation of Fourier transform integrals of basis function products. Since these functions are usually Cartesian Gaussians, in this communication it is shown that the Fourier integrals can be efficiently calculated by exploiting an extension of the Obara–Saika recurrence formulas, which are successfully used by quantum chemists in the computation of molecular integrals. Implementation and future perspectives of the technique are also discussed.

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11

Mejía-López, J., Ana Mejía-López y J. Mazo-Zuluaga. "Uniaxial magnetic anisotropy energy of bimetallic Co–Ni clusters from a first-principles perspective". Physical Chemistry Chemical Physics 20, n.º 24 (2018): 16528–39. http://dx.doi.org/10.1039/c8cp01372a.

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12

Tu, Chunyun, Weijiang Huang, Sheng Liang, Kui Wang, Qin Tian y Wei Yan. "Combining machine learning and quantum chemical calculations for high-throughput virtual screening of thermally activated delayed fluorescence molecular materials: the impact of selection strategy and structural mutations". RSC Advances 12, n.º 48 (2022): 30962–75. http://dx.doi.org/10.1039/d2ra05643g.

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The combination of machine learning, quantum chemical computation with evolutionary theory (selection and mutation) makes high-throughput virtual screening of organic thermally activated delayed fluorescence molecular materials simple.

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13

Zhang, Ming, Wen Chao Huang, Yan Qin y Zhi Xiong Huang. "Quantum Chemical Calculation of Propylene Oxide Ring-Opening Esterification". Advanced Materials Research 150-151 (octubre de 2010): 1254–57. http://dx.doi.org/10.4028/www.scientific.net/amr.150-151.1254.

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The reaction of Propylene oxide(PO) ring-opening esterification was calculated by Gaussian03. The Density Function Theory (DFT) method was employed to study the geometries of PO and Maleic anhydride(MAH) reaction product obtained with the ethanol induced on the base of B3LYP/6-31G in the paper. The transitional states(Ts1,Ts2) of PO ring-opening esterification were found by TS method and were proved by IRC calculation. The results showed that from the reactant to product, the energy reduced about 799.07093 kJ/mol, The computation result showed that the reaction was exothermic.

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14

Chhatwal, Megha, Anup Kumar, Rinkoo D. Gupta y Satish K. Awasthi. "A pyrene-based optical probe capable of molecular computation using chemical input strings". RSC Advances 5, n.º 64 (2015): 51678–81. http://dx.doi.org/10.1039/c5ra08465b.

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Elucidation of molecular computing by employing a pyrene-based chemosensor with Cu²⁺, Fe³⁺, CN⁻ and H⁺ ions as input stimuli and subsequent quantum yields as output responses.

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15

Siddique, Sabir Ali, Muhammad Arshad, Sabiha Naveed, Muhammad Yasir Mehboob, Muhammad Adnan, Riaz Hussain, Babar Ali, Muhammad Bilal Ahmed Siddique y Xin Liu. "Efficient tuning of zinc phthalocyanine-based dyes for dye-sensitized solar cells: a detailed DFT study". RSC Advances 11, n.º 44 (2021): 27570–82. http://dx.doi.org/10.1039/d1ra04529f.

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We used a quantum chemical approach to investigate the optoelectronic properties of dyes T1–T5 for dye-sensitized solar cells using DFT and TD-DFT computation. The newly designed molecules exhibited outstanding photovoltaic and optoelectronic properties.

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16

Davies, Paul. "Quantum Mechanics and the Origin of Life". Symposium - International Astronomical Union 213 (2004): 237–44. http://dx.doi.org/10.1017/s0074180900193349.

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The race to build a quantum computer has led to a radical re-evaluation of the concept of information. In this paper I conjecture that life, defined as an information processing and replicating system, may be exploiting the considerable efficiency advantages offered by quantum computation, and that quantum information processing may dramatically shorten the odds for life originating from a random chemical soup. The plausibility of this conjecture rests, however, on life somehow circumventing the decoherence effects of the environment. I offer some speculations on ways in which this might happen.

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17

Lino, Jéssica Boreli dos Reis, Mateus Aquino Gonçalves, Stephan P. A. Sauer y Teodorico Castro Ramalho. "Extending NMR Quantum Computation Systems by Employing Compounds with Several Heavy Metals as Qubits". Magnetochemistry 8, n.º 5 (21 de abril de 2022): 47. http://dx.doi.org/10.3390/magnetochemistry8050047.

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Nuclear magnetic resonance (NMR) is a spectroscopic method that can be applied to several areas. Currently, this technique is also being used as an experimental quantum simulator, where nuclear spins are employed as quantum bits or qubits. The present work is devoted to studying heavy metal complexes as possible candidates to act as qubit molecules. Nuclei such 113Cd, 199Hg, 125Te, and 77Se assembled with the most common employed nuclei in NMR-QIP implementations (1H, 13C, 19F, 29Si, and 31P) could potentially be used in heteronuclear systems for NMR-QIP implementations. Hence, aiming to contribute to the development of future scalable heteronuclear spin systems, we specially designed four complexes, based on the auspicious qubit systems proposed in our previous work, which will be explored by quantum chemical calculations of their NMR parameters and proposed as suitable qubit molecules. Chemical shifts and spin–spin coupling constants in four complexes were examined using the spin–orbit zeroth-order regular approximation (ZORA) at the density functional theory (DFT) level, as well as the relaxation parameters (T1 and T2). Examining the required spectral properties of NMR-QIP, all the designed complexes were found to be promising candidates for qubit molecules.

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18

Adhikari, Puja, Bahaa Jawad, Rudolf Podgornik y Wai-Yim Ching. "Quantum Chemical Computation of Omicron Mutations Near Cleavage Sites of the Spike Protein". Microorganisms 10, n.º 10 (10 de octubre de 2022): 1999. http://dx.doi.org/10.3390/microorganisms10101999.

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The attachment of the spike protein in SARS-CoV-2 to host cells and the initiation of viral invasion are two critical processes in the viral infection and transmission in which the presence of unique furin (S1/S2) and TMPRSS2 (S2′) cleavage sites play a pivotal role. We provide a detailed analysis of the impact of the BA.1 Omicron mutations vicinal to these cleavage sites using a novel computational method based on the amino acid–amino acid bond pair unit (AABPU), a specific protein structural unit as a proxy for quantifying the atomic interaction. Our study is focused mainly on the spike region between subdomain 2 (SD2) and the central helix (CH), which contains both S1/S2 and S2’ cleavage sites. Based on ab initio quantum calculations, we have identified several key features related to the electronic structure and bonding of the Omicron mutations that significantly increase the size of the relevant AABPUs and the positive charge. These findings enable us to conjecture on the biological role of Omicron mutations and their specific effects on cleavage sites and identify the principles that can be of some value in analyzing new variants.

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19

Čížek, J., F. Vinette y E. J. Weniger. "ON THE USE OF THE SYMBOLIC LANGUAGE MAPLE IN PHYSICS AND CHEMISTRY: SEVERAL EXAMPLES". International Journal of Modern Physics C 04, n.º 02 (abril de 1993): 257–70. http://dx.doi.org/10.1142/s0129183193000276.

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The purpose of this paper is to present several physical and chemical applications of the symbolic computation language Maple which has been developed by the Symbolic Computation Group at the University of Waterloo. The paper will highlight the activity of the Quantum Theory Group of the Department of Applied Mathematics at the University of Waterloo during the years 1985–1992, which has already led to more than 20 articles on applications of Maple. Special attention will be given to examples from quantum mechanics and quantum chemistry: the application of the inner projection technique to anharmonic oscillators yielding explicit expressions for Löwdin's approximants as well as to simple many-electron problem, the use of hypervirial and Hellmann-Feynman theorems for the computation of perturbation series coefficients in rational arithmetics, the creation of coupled-cluster equations by the computer, the use of several techniques including the method of Weniger for the summation of divergent series as they occur in perturbation expansions for anharmonic oscillators or in heat conduction with nonlinear boundary conditions. In all these examples, the symbolic computation language Maple proved to be very useful, and in many cases, it was actually indispensable for obtaining a solution or for keeping control of the accuracy.

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20

Ásgeirsson, Vilhjálmur, Christoph A. Bauer y Stefan Grimme. "Quantum chemical calculation of electron ionization mass spectra for general organic and inorganic molecules". Chemical Science 8, n.º 7 (2017): 4879–95. http://dx.doi.org/10.1039/c7sc00601b.

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The implementation of a novel tight-binding Hamiltonian within the QCEIMS program allows the first-principles based computation of EI mass spectra within a few hours for systems containing elements up to Z = 86.

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21

Cao, Jianshu. "Quantum coherence in nonlinear optical processes: theory and possible application to control of chemical reaction and quantum computation". Journal of Luminescence 87-89 (mayo de 2000): 30–34. http://dx.doi.org/10.1016/s0022-2313(99)00210-0.

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22

Gholami, Samira, Laura Pedraza-González, Xuchun Yang, Alexander A. Granovsky, Ilya N. Ioffe y Massimo Olivucci. "Multistate Multiconfiguration Quantum Chemical Computation of the Two-Photon Absorption Spectra of Bovine Rhodopsin". Journal of Physical Chemistry Letters 10, n.º 20 (23 de septiembre de 2019): 6293–300. http://dx.doi.org/10.1021/acs.jpclett.9b02291.

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23

Breuer, Marian, Piotr Zarzycki, Liang Shi, Thomas A. Clarke, Marcus J. Edwards, Julea N. Butt, David J. Richardson et al. "Molecular structure and free energy landscape for electron transport in the decahaem cytochrome MtrF". Biochemical Society Transactions 40, n.º 6 (21 de noviembre de 2012): 1198–203. http://dx.doi.org/10.1042/bst20120139.

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The free energy profile for electron flow through the bacterial decahaem cytochrome MtrF has been computed using thermodynamic integration and classical molecular dynamics. The extensive calculations on two versions of the structure help to validate the method and results, because differences in the profiles can be related to differences in the charged amino acids local to specific haem groups. First estimates of reorganization free energies λ yield a range consistent with expectations for partially solvent-exposed cofactors, and reveal an activation energy range surmountable for electron flow. Future work will aim at increasing the accuracy of λ with polarizable forcefield dynamics and quantum chemical energy gap calculations, as well as quantum chemical computation of electronic coupling matrix elements.

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24

Yang, Jun, Weifeng Hu, Denis Usvyat, Devin Matthews, Martin Schütz y Garnet Kin-Lic Chan. "Ab initio determination of the crystalline benzene lattice energy to sub-kilojoule/mole accuracy". Science 345, n.º 6197 (7 de agosto de 2014): 640–43. http://dx.doi.org/10.1126/science.1254419.

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Computation of lattice energies to an accuracy sufficient to distinguish polymorphs is a fundamental bottleneck in crystal structure prediction. For the lattice energy of the prototypical benzene crystal, we combined the quantum chemical advances of the last decade to attain sub-kilojoule per mole accuracy, an order-of-magnitude improvement in certainty over prior calculations that necessitates revision of the experimental extrapolation to 0 kelvin. Our computations reveal the nature of binding by improving on previously inaccessible or inaccurate multibody and many-electron contributions and provide revised estimates of the effects of temperature, vibrations, and relaxation. Our demonstration raises prospects for definitive first-principles resolution of competing polymorphs in molecular crystal structure prediction.

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25

Chan, Bun. "How to computationally calculate thermochemical properties objectively, accurately, and as economically as possible". Pure and Applied Chemistry 89, n.º 6 (27 de junio de 2017): 699–713. http://dx.doi.org/10.1515/pac-2016-1116.

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Abstract We have developed the WnX series of quantum chemistry composite protocols for the computation of highly-accurate thermochemical quantities with advanced efficiency and applicability. The W1X-type methods have a general accuracy of ~3–4 kJ mol−1 and they can currently be applied to systems with ~20–30 atoms. Higher-level methods include W2X, W3X and W3X-L, with the most accurate of these being W3X-L. It can be applied to molecules with ~10–20 atoms and is generally accurate to ~1.5 kJ mol−1. The WnX procedures have opened up new possibilities for computational chemists in pursue of accurate thermochemical values in a highly-productive manner.

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26

Zhang, Ming, Zhi Xiong Huang y Yan Qin. "Quantum Chemical Calculation of Maleic Anhydride Ring-Opening Reaction". Advanced Materials Research 79-82 (agosto de 2009): 1193–96. http://dx.doi.org/10.4028/www.scientific.net/amr.79-82.1193.

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The reaction of maleic anhydride ring-opening was calculated by Gaussian03. The Density Function Theory (DFT) method were employed to study the geometries of maleic anhydride and ethanol on the base of B3LYP/6-31G in the paper. The transitional states(Ts1,Ts2) of maleic anhydride ring-opening reaction were found by TS method and were proved by IRC calculation. The results showed that from the reactant to product, the energy reduced about 129.25337kJ/mol,The computation results showed that the reaction was exothermic and matched up well with experiment. Nowadays the MAH multipolymers were studied extensively.Because of C=C double bond has double substitutions and the great Spatial steric hindrance, MAH was always regarded as representative that couldn’t carry out homopolymerization[1,2]. Much attention has been paid to MAH polymerization(Homopolymerization[4] and Copolymerization[5-15])gradually Long and his colleagues[3] published papers on MAH homopolymerization in 1963. The related reports have been increased since MAH multipolymer was found to possess anti-tumor and biological activity[16]. According to the polymerization mechanism，epoxide ring-opening esterification were divided into three kinds: cationic polymerization, anionic polymerization and coordination polymerization.The saturated polyesters were prepared through maleic anhydride and alkene oxide reaction, generally using anionic polymerization initiated by hydroxyl compound such as alcohol, water and carboxylic acid. maleic anhydride ring-opening reaction initiated by alcohol(Eq. 1) was discussed in this paper.

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Wacławek, Stanisław. "Do We Still Need a Laboratory to Study Advanced Oxidation Processes? A Review of the Modelling of Radical Reactions used for Water Treatment". Ecological Chemistry and Engineering S 28, n.º 1 (1 de marzo de 2021): 11–28. http://dx.doi.org/10.2478/eces-2021-0002.

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Abstract Environmental pollution due to humankind’s often irresponsible actions has become a serious concern in the last few decades. Numerous contaminants are anthropogenically produced and are being transformed in ecological systems, which creates pollutants with unknown chemical properties and toxicity. Such chemical pathways are usually examined in the laboratory, where hours are often needed to perform proper kinetic experiments and analytical procedures. Due to increased computing power, it becomes easier to use quantum chemistry computation approaches (QCC) for predicting reaction pathways, kinetics, and regioselectivity. This review paper presents QCC for describing the oxidative degradation of contaminants by advanced oxidation processes (AOP, i.e., techniques utilizing •OH for degradation of pollutants). Regioselectivity was discussed based on the Acid Blue 129 compound. Moreover, the forecasting of the mechanism of hydroxyl radical reaction with organic pollutants and the techniques of prediction of degradation kinetics was discussed. The reactions of •OH in various aqueous systems (explicit and implicit solvation) with water matrix constituents were reviewed. For example, possible singlet oxygen formation routes in the AOP systems were proposed. Furthermore, quantum chemical computation was shown to be an excellent tool for solving the controversies present in the field of environmental chemistry, such as the Fenton reaction debate [main species were determined to be: •OH < pH = 2.2 < oxoiron(IV)]. An ongoing discussion on such processes concerning similar reactions, e.g., associated with sulphate radical-based advanced oxidation processes (SR-AOP), could, in the future, be enriched by similar means. It can be concluded that, with the rapid growth of computational power, QCC can replace most of the experimental investigations related to the pollutant’s remediation in the future; at the same time, experiments could be pushed aside for quality assessment only.

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Gribben, Jordan, Timothy R. Wilson y Mark E. Eberhart. "Unicorns, Rhinoceroses and Chemical Bonds". Molecules 28, n.º 4 (12 de febrero de 2023): 1746. http://dx.doi.org/10.3390/molecules28041746.

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The nascent field of computationally aided molecular design will be built around the ability to make computation useful to synthetic chemists who draw on their empirically based chemical intuition to synthesize new and useful molecules. This fact poses a dilemma, as much of existing chemical intuition is framed in the language of chemical bonds, which are pictured as possessing physical properties. Unfortunately, it has been posited that calculating these bond properties is impossible because chemical bonds do not exist. For much of the computational-chemistry community, bonds are seen as mythical—the unicorns of the chemical world. Here, we show that this is not the case. Using the same formalism and concepts that illuminated the atoms in molecules, we shine light on the bonds that connect them. The real space analogue of the chemical bond becomes the bond bundle in an extended quantum theory of atoms in molecules (QTAIM). We show that bond bundles possess all the properties typically associated with chemical bonds, including an energy and electron count. In addition, bond bundles are characterized by a number of nontraditional attributes, including, significantly, a boundary. We show, with examples drawn from solid state and molecular chemistry, that the calculated properties of bond bundles are consistent with those that nourish chemical intuition. We go further, however, and show that bond bundles provide new and quantifiable insights into the structure and properties of molecules and materials.

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ZHANG, D. W. y J. Z. H. ZHANG. "FULL AB INITIO COMPUTATION OF PROTEIN-WATER INTERACTION ENERGIES". Journal of Theoretical and Computational Chemistry 03, n.º 01 (marzo de 2004): 43–49. http://dx.doi.org/10.1142/s0219633604000891.

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A method to perform full quantum mechanical (ab initio) calculation of interaction energy involving a macromolecule like protein has recently been developed. This new scheme, named molecular fractionation with conjugate caps (MFCC), decomposes a protein molecule into amino acid-based fragments. These individual fragments are properly treated to preserve the chemical property of the bonds that are cut. Through proper combination of interaction energies between the molecule and individual fragments and their conjugate caps, the full protein-molecule interaction energy can be obtained to a high degree-of-accuracy by full ab initio calculations. Here we report a benchmark full ab initio calculation of interaction energy between a HIV-1 gp41 protein (with 982 atoms) and a water molecule at various geometries using HF (Hartree Fock), DFT (density functional theory) and MP2 (second-order Moller-Plesset perturbation theory) methods on a standard workstation.

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Poo, Mu-ming y Ling Wang. "Andrew Chi-Chih Yao: the future of quantum computing". National Science Review 5, n.º 4 (26 de abril de 2018): 598–602. http://dx.doi.org/10.1093/nsr/nwy042.

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ABSTRACT Quantum computing and quantum computers have attracted much attention from both the academic community and industry in recent years. By exploiting the quantum properties of materials, scientists are aiming to overcome Moore's law of miniaturization and develop novel quantum computers. The concept of quantum computing was first introduced by the distinguished physicist Richard Feynman in 1981. As one of the early pioneers in this field, Turing Award laureate Andrew Chi-Chih Yao made a seminal contribution in developing the theoretical basis for quantum computation in 1993. Since 2011, he has served as the founding director of Tsinghua University's Center for Quantum Information (CQI), which aims to become a world-class research center for quantum computing. In a recent interview with NSR, Yao recounted the history of quantum computing and expressed his view on the future of this field. He suggests that quantum computers could excel in many tasks such as the design of new materials and drugs as well as in the simulation of chemical reactions, but they may not supersede traditional computers in tasks for which traditional computers are already proven to be highly efficient.

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31

Fioroni, Marco y Nathan J. DeYonker. "Siloxyl radical initiated HCN polymerization: computation of N-heterocycles formation and surface passivation". Monthly Notices of the Royal Astronomical Society 512, n.º 2 (4 de febrero de 2022): 1629–38. http://dx.doi.org/10.1093/mnras/stac271.

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ABSTRACT In this work, by means of quantum chemistry (Density Functional Theory (DFT), PW6B95/def2-TZVPP; DLPNO-CCSD(T)/CBS), HCN polymerization [(HCN)1 − 4] initiated and catalysed by a siloxyl radical (Si-O•) on a model silica surface is analysed. Linear HCN polymers (pHCN) are obtained by a radical initiated mechanism at a SiO• site and are characterized by a -(HC-N)- skeleton due to radical localization on the terminal N atom and radical attack on the C centre. NC heterocycles are formed by cyclization of the linear SiO-(HCN)3 − 4 and are always thermodynamically preferred over their linear counterparts, acting as thermodynamic sinks. Of particular interest to the astrochemistry community is the formation of the N-heterocycle 1,3,5-triazine that can be released into the gas phase at relatively low T (ΔG† = 23.3 kcal/mol). Full hydrogenation of SiO-(HCN•) follows two reaction channels with products: (a) SiO-CH3 + •NH2 or (b) amino-methanol + Si•, though characterized by slow kinetics. Nucleophilic addition of H2O to the electron-rich SiO-(HCN•) shows an unfavourable thermodynamics as well as a high-activation energy. The cleavage of the linear (HCN)1−4 from the SiO• site also shows a high thermodynamic energy penalty (ΔG≥82.0 kcal/mol). As a consequence, the silicate surface will be passivated by a chemically active ‘pHCN brush’ modifying the surface physico-chemical properties. The prospect of surface-catalysed HCN polymers exhibiting a high degree of chemical reactivity and proposed avenues for the formation of 1,3,5-triazine and amino-methanol opens exciting new chemical pathways to Complex Organic Matter formation in astrochemistry.

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32

Nakaji, Kouhei, Suguru Endo, Yuichiro Matsuzaki y Hideaki Hakoshima. "Measurement optimization of variational quantum simulation by classical shadow and derandomization". Quantum 7 (4 de mayo de 2023): 995. http://dx.doi.org/10.22331/q-2023-05-04-995.

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Simulating large quantum systems is the ultimate goal of quantum computing. Variational quantum simulation (VQS) gives us a tool to achieve the goal in near-term devices by distributing the computation load to both classical and quantum computers. However, as the size of the quantum system becomes large, the execution of VQS becomes more and more challenging. One of the most severe challenges is the drastic increase in the number of measurements; for example, the number of measurements tends to increase by the fourth power of the number of qubits in a quantum simulation with a chemical Hamiltonian. This work aims to dramatically decrease the number of measurements in VQS by recently proposed shadow-based strategies such as classical shadow and derandomization. Even though previous literature shows that shadow-based strategies successfully optimize measurements in the variational quantum optimization (VQO), how to apply them to VQS was unclear due to the gap between VQO and VQS in measuring observables. In this paper, we bridge the gap by changing the way of measuring observables in VQS and propose an algorithm to optimize measurements in VQS by shadow-based strategies. Our theoretical analysis not only reveals the advantage of using our algorithm in VQS but theoretically supports using shadow-based strategies in VQO, whose advantage has only been given numerically. Additionally, our numerical experiment shows the validity of using our algorithm with a quantum chemical system.

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33

Nisha, S. V. D. y I. Hubert Joe. "Quantum chemical computation and spectroscopic investigation on antiviral drug Acyclovir:-In-silico and in-vitro analysis". Journal of Molecular Structure 1233 (junio de 2021): 130033. http://dx.doi.org/10.1016/j.molstruc.2021.130033.

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34

Ohyama, Junya, Jumpei Shibano, Atsushi Satsuma, Ryoichi Fukuda, Yuta Yamamoto, Shigeo Arai, Tetsuya Shishido, Hiroyuki Asakura, Saburo Hosokawa y Tsunehiro Tanaka. "Quantum Chemical Computation-Driven Development of Cu-Shell–Ru-Core Nanoparticle Catalyst for NO Reduction Reaction". Journal of Physical Chemistry C 123, n.º 33 (25 de julio de 2019): 20251–56. http://dx.doi.org/10.1021/acs.jpcc.9b03687.

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35

Pankratov, Alexei. "Use of semiempirical quantum chemical approaches in computation of molecular dipole moments of tropones and tropolones". Journal of the Serbian Chemical Society 65, n.º 1 (2000): 1–13. http://dx.doi.org/10.2298/jsc0001001p.

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Using the MNDO, AM1 and PM3 methods, the dipole moments (m) of 28 tropones and 34 tropolones molecules have been computed. The potentials of the above approaches for the evaluation of m have been revealed. The correlations mexper = bmtheor have been established.

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36

Nilforoushan, Niloufar, Michele Casula, Adriano Amaricci, Marco Caputo, Jonathan Caillaux, Lama Khalil, Evangelos Papalazarou et al. "Moving Dirac nodes by chemical substitution". Proceedings of the National Academy of Sciences 118, n.º 33 (12 de agosto de 2021): e2108617118. http://dx.doi.org/10.1073/pnas.2108617118.

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Dirac fermions play a central role in the study of topological phases, for they can generate a variety of exotic states, such as Weyl semimetals and topological insulators. The control and manipulation of Dirac fermions constitute a fundamental step toward the realization of novel concepts of electronic devices and quantum computation. By means of Angle-Resolved Photo-Emission Spectroscopy (ARPES) experiments and ab initio simulations, here, we show that Dirac states can be effectively tuned by doping a transition metal sulfide, BaNiS2, through Co/Ni substitution. The symmetry and chemical characteristics of this material, combined with the modification of the charge-transfer gap of BaCo1−xNixS2 across its phase diagram, lead to the formation of Dirac lines, whose position in k-space can be displaced along the Γ−M symmetry direction and their form reshaped. Not only does the doping x tailor the location and shape of the Dirac bands, but it also controls the metal-insulator transition in the same compound, making BaCo1−xNixS2 a model system to functionalize Dirac materials by varying the strength of electron correlations.

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37

Kesorn, Aniwat, Rutchapon Hunkao, Kritsanu Tivakornsasithorn, Asawin Sinsarp, Worasak Sukkabot y Sujin Suwanna. "Dynamical Behavior of Two Interacting Double Quantum Dots in 2D Materials for Feasibility of Controlled-NOT Operation". Nanomaterials 12, n.º 20 (13 de octubre de 2022): 3599. http://dx.doi.org/10.3390/nano12203599.

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Two interacting double quantum dots (DQDs) can be suitable candidates for operation in the applications of quantum information processing and computation. In this work, DQDs are modeled by the heterostructure of two-dimensional (2D) MoS2 having 1T-phase embedded in 2H-phase with the aim to investigate the feasibility of controlled-NOT (CNOT) gate operation with the Coulomb interaction. The Hamiltonian of the system is constructed by two models, namely the 2D electronic potential model and the 4×4 matrix model whose matrix elements are computed from the approximated two-level systems interaction. The dynamics of states are carried out by the Crank–Nicolson method in the potential model and by the fourth order Runge–Kutta method in the matrix model. Model parameters are analyzed to optimize the CNOT operation feasibility and fidelity, and investigate the behaviors of DQDs in different regimes. Results from both models are in excellent agreement, indicating that the constructed matrix model can be used to simulate dynamical behaviors of two interacting DQDs with lower computational resources. For CNOT operation, the two DQD systems with the Coulomb interaction are feasible, though optimization of engineering parameters is needed to achieve optimal fidelity.

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38

Martyn, John M., Yuan Liu, Zachary E. Chin y Isaac L. Chuang. "Efficient fully-coherent quantum signal processing algorithms for real-time dynamics simulation". Journal of Chemical Physics 158, n.º 2 (14 de enero de 2023): 024106. http://dx.doi.org/10.1063/5.0124385.

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Simulating the unitary dynamics of a quantum system is a fundamental problem of quantum mechanics, in which quantum computers are believed to have significant advantage over their classical counterparts. One prominent such instance is the simulation of electronic dynamics, which plays an essential role in chemical reactions, non-equilibrium dynamics, and material design. These systems are time- dependent, which requires that the corresponding simulation algorithm can be successfully concatenated with itself over different time intervals to reproduce the overall coherent quantum dynamics of the system. In this paper, we quantify such simulation algorithms by the property of being fully-coherent: the algorithm succeeds with arbitrarily high success probability 1 − δ while only requiring a single copy of the initial state. We subsequently develop fully-coherent simulation algorithms based on quantum signal processing (QSP), including a novel algorithm that circumvents the use of amplitude amplification while also achieving a query complexity additive in time t, ln(1/ δ), and ln(1/ ϵ) for error tolerance ϵ: [Formula: see text]. Furthermore, we numerically analyze these algorithms by applying them to the simulation of the spin dynamics of the Heisenberg model and the correlated electronic dynamics of an H2 molecule. Since any electronic Hamiltonian can be mapped to a spin Hamiltonian, our algorithm can efficiently simulate time-dependent ab initio electronic dynamics in the circuit model of quantum computation. Accordingly, it is also our hope that the present work serves as a bridge between QSP-based quantum algorithms and chemical dynamics, stimulating a cross-fertilization between these exciting fields.

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39

Lahoz-Beltra, Rafael. "Solving the Schrödinger Equation with Genetic Algorithms: A Practical Approach". Computers 11, n.º 12 (27 de noviembre de 2022): 169. http://dx.doi.org/10.3390/computers11120169.

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The Schrödinger equation is one of the most important equations in physics and chemistry and can be solved in the simplest cases by computer numerical methods. Since the beginning of the 1970s, the computer began to be used to solve this equation in elementary quantum systems, and, in the most complex case, a ‘hydrogen-like’ system. Obtaining the solution means finding the wave function, which allows predicting the physical and chemical properties of the quantum system. However, when a quantum system is more complex than a ‘hydrogen-like’ system, we must be satisfied with an approximate solution of the equation. During the last decade, application of algorithms and principles of quantum computation in disciplines other than physics and chemistry, such as biology and artificial intelligence, has led to the search for alternative techniques with which to obtain approximate solutions of the Schrödinger equation. In this work, we review and illustrate the application of genetic algorithms, i.e., stochastic optimization procedures inspired by Darwinian evolution, in elementary quantum systems and in quantum models of artificial intelligence. In this last field, we illustrate with two ‘toy models’ how to solve the Schrödinger equation in an elementary model of a quantum neuron and in the synthesis of quantum circuits controlling the behavior of a Braitenberg vehicle.

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40

Janoschek, Rudolf. "Quantum chemical B3LYP/cc-pvqz computation of ground-state structures and properties of small molecules with atoms of Z ≤ 18 (hydrogen to argon)(IUPAC Technical Report)". Pure and Applied Chemistry 73, n.º 9 (1 de septiembre de 2001): 1521–53. http://dx.doi.org/10.1351/pac200173091521.

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Since density functional theory (DFT) achieved a remarkable break-through in computational chemistry, the important general question "How reliable are quantum chemical calculations for spectroscopic properties?" should be answered anew. In this project, the most successful density functionals, namely the Becke B3LYP functionals, and the correlation-consistent polarized valence quadruple zeta basis sets (cc-pvqz) are applied to small molecules. In particular, the complete set of experimentally known diatomic molecules formed by the atoms H to Ar (these are 214 species) is uniformly calculated, and calculated spectroscopic properties are compared with experimental ones. Computationally demanding molecules, such as open-shell systems, anions, or noble gas compounds, are included in this study. Investigated spectroscopic properties are spectroscopic ground state, equilibrium internuclear distance, harmonic vibrational wavenumber, anharmonicity, vibrational absolute absorption intensity, electric dipole moment, ionization potential, and dissociation energy. The same computational method has also been applied to the ground-state geometries of 56 polyatomic molecules up to the size of benzene. Special sections are dedicated to nuclear magnetic resonance (NMR) chemical shifts and isotropic hyperfine coupling constants. Each set of systems for a chosen property is statistically analyzed, and the above important question "How reliable...?" is mathematically answered by the mean absolute deviation between calculated and experimental data, as well as by the worst agreement. In addition to presentation of numerous quantum chemically calculated spectroscopic properties, a corresponding updated list of references for experimentally determined properties is presented.

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41

Igbafe, A. I. y O. F. Omobude. "Theoretical Rate Evaluation of Gas Phase Atmospheric Ozone Reactions". Advanced Materials Research 367 (octubre de 2011): 849–52. http://dx.doi.org/10.4028/www.scientific.net/amr.367.849.

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The rate of transformation of ozone in the troposphere over a temperature range of-100°C and +100°C has been established. Tropospheric ozone with the quality of a strong oxidizing agent, is secondary pollutant species associated with the initiation of numerous chemical reactions in the atmosphere. In this study, a theoretical approach utilized Gibb’s free energy of reaction and enthalpy of reaction in transition state theory model equations to generate chemical equilibrium data and consequently reaction kinetic parameters. The thermochemical properties were obtained using electronic structural methods of the quantum mechanics computational chemistries which approximates the Schrödinger equation. The model chemistry methods were evaluated using the GuassView for generating molecular structures of species and the Gaussian 03 (G03) package for energy computation. The study revealed that the most relevant of the reactions considered was that involving NO with a rate constant of 7.39 x 1011 s-1 and energy of activation (EA/R) of-216.98 K while the least involved HS* with rate constant of 9.56 x 1069 s-1 and energy of activation (EA/R) of-202.95 K.

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42

Sha, Linxiu y Zhongqi Pan. "FSQGA based 3D complexity wellbore trajectory optimization". Oil & Gas Sciences and Technology – Revue d’IFP Energies nouvelles 73 (2018): 79. http://dx.doi.org/10.2516/ogst/2018008.

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Determination of the trajectory of a complex wellbore is very challenging due to the variety of possible well types, as well as the numerous complicated drilling variables and constraints. The well type could be directional wells, cluster wells, horizontal wells, extended reach wells, redrilling wells, and complex structure wells, etc. The drilling variables and constraints include wellbore length, inclination hold angles, azimuth angles, dogleg severity, true vertical depths, lateral length, casing setting depths, and true vertical depth. In this paper, we propose and develop an improved computational model based on Fibonacci sequence to adjust the quantum rotation step in quantum genetic algorithm for achieving cost-efficient complex wellbore trajectories. By using Fibonacci sequence based quantum genetic algorithm (FSQGA) in a complex searching problem, we can find high-quality globally optimal solutions with high speed through a parallel process. The simulation results show that FSQGA can significantly reduce computation complexity, and reach minimum objection values faster. Meanwhile, minimization of the true measurement depth of complex wellbore trajectory in actual gas-oil field shows that the drilling cost can be reduced up to 4.65%. We believe this new algorithm has the potential to improve drilling efficiency, to reduce the drilling time and drilling cost in real-time wellbore trajectory control.

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43

Thibi Mol, K., T. F. Abbs Fen Reji y H. Marshan Robert. "Synthesis, spectroscopic investigation and quantum chemical computation of 2-(2-arylamino-4-aminothiazol-5-oyl) naphthalene derivatives". Journal of Crystal Growth 583 (abril de 2022): 126553. http://dx.doi.org/10.1016/j.jcrysgro.2022.126553.

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44

Pan, Xiaoliang, Pengfei Li, Junming Ho, Jingzhi Pu, Ye Mei y Yihan Shao. "Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching". Physical Chemistry Chemical Physics 21, n.º 37 (2019): 20595–605. http://dx.doi.org/10.1039/c9cp02593f.

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An efficient and accurate reference potential simulation protocol is proposed for producing ab initio quantum mechanical/molecular mechanical (AI-QM/MM) quality free energy profiles for chemical reactions in a solvent or macromolecular environment.

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45

Mol, G. P. Sheeja, D. Aruldhas, I. Hubert Joe y S. Balachandran. "Experimental and theoretical spectroscopic analysis, chemical reactivity and fungicidal activity study on benalaxyl along with quantum chemical computation on metalaxyl and furalaxyl". Chemical Data Collections 17-18 (diciembre de 2018): 370–93. http://dx.doi.org/10.1016/j.cdc.2018.10.005.

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46

Kumar, Sunil. "Numerical Computation of Time-Fractional Fokker–Planck Equation Arising in Solid State Physics and Circuit Theory Numerical Computation of Time-Fractional Fokker–Planck Equation Arising in Solid State Physics and Circuit Theory". Zeitschrift für Naturforschung A 68, n.º 12 (1 de diciembre de 2013): 777–84. http://dx.doi.org/10.5560/zna.2013-0057.

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The main aim of the present work is to propose a new and simple algorithm to obtain a quick and accurate analytical solution of the time fractional Fokker-Plank equation which arises in various fields in natural science, including solid-state physics, quantum optics, chemical physics, theoretical biology, and circuit theory. This new and simple algorithm is an innovative adjustment in Laplace transform algorithm which makes the calculations much simpler and applicable to several practical problems in science and engineering. The proposed scheme finds the solutions without any discretization or restrictive assumptions and is free from round-off errors and therefore reduces the numerical computations to a great extent. Furthermore, several numerical examples are presented to illustrate the accuracy and the stability of the method.

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47

Petrone, Alessio, Fulvio Perrella, Federico Coppola, Luigi Crisci, Greta Donati, Paola Cimino y Nadia Rega. "Ultrafast photo-induced processes in complex environments: The role of accuracy in excited-state energy potentials and initial conditions". Chemical Physics Reviews 3, n.º 2 (junio de 2022): 021307. http://dx.doi.org/10.1063/5.0085512.

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Light induces non-equilibrium time evolving molecular phenomena. The computational modeling of photo-induced processes in large systems, embedded in complex environments (i.e., solutions, proteins, materials), demands for a quantum and statistical mechanic treatment to achieve the required accuracy in the description of both the excited-state energy potentials and the choice of the initial conditions for dynamical simulations. On the other hand, the theoretical investigation on the atomistic scale of times and sizes of the ultrafast photo-induced reactivity and non-equilibrium relaxation dynamics right upon excitation requests tailored computational protocols. These methods often exploit hierarchic computation schemes, where a large part of the degrees of freedom are required to be treated explicitly to achieve the right accuracy. Additionally, part of the explicit system needs to be treated at ab initio level, where density functional theory, using hybrid functionals, represents a good compromise between accuracy and computational cost, when proton transfers, non-covalent interactions, and hydrogen bond dynamics play important roles. Thus, the modeling strategies presented in this review stress the importance of hierarchical quantum/molecular mechanics with effective non-periodic boundary conditions and efficient phase-sampling schemes to achieve chemical accuracy in ultrafast time-resolved spectroscopy and photo-induced phenomena. These approaches can allow explicit and accurate treatment of molecule/environment interactions, including also the electrostatic and dispersion forces of the bulk. At the same time, the specificities of the different case studies of photo-induced phenomena in solutions and biological environments are highlighted and discussed, with special attention to the computational and modeling challenges.

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48

Hameroff, Stuart. "The neuron doctrine is an insult to neurons". Behavioral and Brain Sciences 22, n.º 5 (octubre de 1999): 838–39. http://dx.doi.org/10.1017/s0140525x9931219x.

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As presently implemented, the neuron doctrine (ND) portrays the brain's neurons and chemical synapses as fundamental components in a computer-like switching circuit, supporting a view of brain = mind = computer. However, close examination reveals individual neurons to be far more complex than simple switches, with enormous capacity for intracellular information processing (e.g., in the internal cytoskeleton). Other poorly appreciated factors (gap junctions, apparent randomness, dendritic-dendritic processing, possible quantum computation, the living state) also suggest that the ND grossly oversimplifies neuronal functions. In the quest to understand consciousness, the presently implemented ND may throw out the baby with the bath water.

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49

Gražulis, Saulius, Andrius Merkys, Antanas Vaitkus, Armel Le Bail, Daniel Chateigner, Linas Vilčiauskas, Stefaan Cottenier, Torbjörn Björkman y Peter Murray-Rust. "Launching the Theoretical Crystallography Open Database". Acta Crystallographica Section A Foundations and Advances 70, a1 (5 de agosto de 2014): C1736. http://dx.doi.org/10.1107/s2053273314082631.

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As computational chemistry methods enjoy unprecedented growth, computer power increases and price/performance ratio drops, a large number of crystal structures can today be refined and their properties computed using modern theoretical approaches, such as DFT, post-HF, QM/MM, MCMM methods. Availability of several open source codes for computational and quantum chemistry and open-access crystallographic databases enables large scale computations of material structures and properties. We thus increasingly feel that an open collection of theoretically computed chemical structures would be a valuable resource for the scientific community. To address this need, we have launched a Theoretical Crystallography Open Database (TCOD, http://www.crystallography.net/tcod/). The TCOD sets a goal to collect a comprehensive set of computed crystal structures that would be made available under an Open Data license and invites all scientists to deposit their published results or pre-publication data. Accompanied with a large set of experimental structures in the COD database [1], the TCOD opens immediate possibilities for experimental and theoretical data cross-validation. To ensure high quality of deposited data, TCOD offers ontologies in a form of CIF [2] dictionaries that describe parameters of computed chemical and crystal structures, and an automated pipeline that checks each submitted structure against a set of community-specified criteria for convergence, computation quality and reproducibility. The scope of TCOD and validation tools make TCOD a high-quality, comprehensive theoretical structure database, useful in a broad range of disciplines. First-principle calculations are also of huge interest to simulate physical properties, either prospectively or for materials that do not grow as sufficiently large crystals. The property results can now be tested against the Material Properties Open Database [3] (http://www.materialproperties.org/) to ameliorate the used models.

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50

Jähnigen, Sascha y Daniel Sebastiani. "Carbon Atoms Speaking Out: How the Geometric Sensitivity of 13C Chemical Shifts Leads to Understanding the Colour Tuning of Phycocyanobilin in Cph1 and AnPixJ". Molecules 25, n.º 23 (24 de noviembre de 2020): 5505. http://dx.doi.org/10.3390/molecules25235505.

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We present a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics–statistical approach for the interpretation of nuclear magnetic resonance (NMR) chemical shift patterns in phycocyanobilin (PCB). These were originally associated with colour tuning upon photoproduct formation in red/green-absorbing cyanobacteriochrome AnPixJg2 and red/far-red-absorbing phytochrome Cph1Δ2. We pursue an indirect approach without computation of the absorption frequencies since the molecular geometry of cofactor and protein are not accurately known. Instead, we resort to a heuristic determination of the conjugation length in PCB through the experimental NMR chemical shift patterns, supported by quantum chemical calculations. We have found a characteristic correlation pattern of 13C chemical shifts to specific bond orders within the π-conjugated system, which rests on the relative position of carbon atoms with respect to electron-withdrawing groups and the polarisation of covalent bonds. We propose the inversion of this regioselective relationship using multivariate statistics and to apply it to the known experimental NMR chemical shifts in order to predict changes in the bond alternation pattern. Therefrom the extent of electronic conjugation, and eventually the change in absorption frequency, can be derived. In the process, the consultation of explicit mesomeric formulae plays an important role to qualitatively account for possible conjugation scenarios of the chromophore. While we are able to consistently associate the NMR chemical shifts with hypsochromic and bathochromic shifts in the Pg and Pfr, our approach represents an alternative method to increase the explanatory power of NMR spectroscopic data in proteins.

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