From Perception to Prediction and Interpretation: Enlightening the Gray Zone of Molecular Bricks of Life With the Help of Machine Learning and Quantum Chemistry

Wiley Interdisciplinary Reviews Computational Molecular Science, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 1, 2025

ABSTRACT The latest developments of a general exploration/exploitation strategy for the computational study molecular bricks life in gas‐phase are presented and illustrated by means prototypical semi‐rigid flexible systems. In first step, generalized natural internal coordinates employed to obtain clear‐cut separation between different degrees freedom, machine‐learning algorithms based on chemical descriptors (synthons) drive fast quantum methods exploration rugged potential energy surfaces ruled soft freedom. Then, models carefully selected exploiting energies, geometries, vibrational frequencies with aim maximizing accuracy overall description while retaining reasonable cost all steps. particular, composite wave‐function method is used whereas double‐hybrid functional geometries harmonic cheaper global hybrid anharmonic contributions. A panel containing up 50 atoms show that proposed draws closer state‐of‐the‐art small molecules, but applicable much larger implementation whole workflow terms preprocessing postprocessing data provided standard electronic structure codes paves way toward accurate yet not prohibitively expensive medium‐ large‐sized molecules user‐friendly black‐box tool exploitable also experiment‐oriented researchers.

Language: Английский

---

Structures and Rotational Constants of Monocyclic Monoterpenes at DFT Cost by Pisa Composite Schemes and Vibrational Perturbation Theory

The Journal of Physical Chemistry A, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 6, 2025

The structures and rotational constants of prototypical monocyclic terpenes terpenoids have been analyzed by a general computational strategy based on recent Pisa composite schemes (PCS) vibrational perturbation theory at second order (VPT2). Concerning equilibrium geometries, one-parameter empirical correction is added to bond lengths obtained the revDSD-PBEP86 double hybrid functional in conjunction with slightly modified cc-pVTZ-F12 basis set. same set give accurate harmonic frequencies, whereas cheaper B3LYP double-ζ employed compute semidiagonal cubic force needed obtain corrections framework VPT2 model. final results this way show most cases average deviations respect experiment close 0.1%, which correspond errors around 1 mÅ 0.1° for valence angles, respectively. accuracy has produced reliable estimates species not yet experimentally. In addition intrinsic interest studied molecules, article confirms that high-resolution spectroscopic studies quite large systems can now be aided very robust user-friendly tool.

Language: Английский

---

Toward Accurate Quantum Chemical Methods for Molecules of Increasing Dimension: The New Family of Pisa Composite Schemes

The Journal of Physical Chemistry A, Journal Year: 2024, Volume and Issue: 128(24), P. 4886 - 4900

Published: June 7, 2024

The new versions of the Pisa composite scheme introduced in present paper are based on careful selection different quantum chemical models for energies, geometries, and vibrational frequencies, with aim maximizing accuracy overall description while retaining a reasonable cost all steps. In particular, computation accurate electronic energies has been further improved introducing more reliable complete basis set extrapolations estimation core–valence correlation, together sets third-row atoms. Furthermore, reduced-cost frozen natural orbital (FNO) model validated large molecules. Accurate molecular structures can be obtained avoiding extrapolation evaluating correlation at MP2 level. Unfortunately, analytical gradients not available FNO version model. Therefore, molecules, an alternative is offered by evaluation valence contributions double-hybrid functional conjunction same contribution or means one-parameter approximation. employed to evaluate zero-point partition functions. After validation small systems, panel bricks life used analyze their performances problems current fundamental technological interest. fully black-box implementation computational workflow paves way toward yet prohibitively expensive study medium- large-sized molecules also experimentally oriented researchers.

Language: Английский

---

Accurate structures and rotational constants of bicyclic monoterpenes at DFT cost by means of the bond-corrected Pisa composite scheme (BPCS)

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 161(1)

Published: July 3, 2024

The structural, conformational, and spectroscopic properties in the gas phase of 20 bicyclic monoterpenes monoterpenoids have been analyzed by a new accurate, reduced-cost computational strategy. In detail, revDSD-PBEP86 double-hybrid functional conjunction with D3BJ empirical dispersion corrections suitable triple-zeta basis set provides accurate geometrical parameters, whence equilibrium rotational constants, which are further improved proper account core–valence correlation. Average deviations within 0.1% between computed experimental constants reached when taking into vibrational obtained B3LYP double-zeta framework second-order perturbation theory. addition to their intrinsic interest, studied terpenes extend panel systems for proposed strategy has provided results at density theory cost. Therefore, very yet robust user-friendly tool is now available systematic investigations role stereo-electronic effects on large current technological and/or biological interest experimentally oriented researchers.

Language: Английский

---

Accurate Geometries of Large Molecules at DFT Cost by Semiexperimental and Coupled Cluster Templating Fragments

Journal of Chemical Theory and Computation, Journal Year: 2024, Volume and Issue: 20(20), P. 9243 - 9258

Published: Oct. 7, 2024

Accurate geometries of small semirigid molecules in the gas phase are available thanks to high-resolution spectroscopy and accurate quantum chemical approaches. These results can be employed for validating cheaper low-level models or correcting corresponding structures large molecules. On these grounds, this work, a panel semiexperimental equilibrium already literature is used confirm average error (1 mÅ bond lengths 2 mrad valence angles) version Pisa composite schemes (PCS2), which applicable containing up about 20 atoms. Then, 30 additional medium-sized systems were optimized at PCS2 level cover more balanced space moieties poorly represented SE compilations. The final database on public domain Web site (https://www.skies-village.it/databases/) larger obtained by hybrid double-hybrid density functionals framework templating molecule approach. Several examples show that corrections based building blocks taken from reduce B3LYP geometrical parameters nearly an order magnitude without increasing computational cost. Furthermore, different functional theory (DFT) wave function (e.g., MP2) improved same way simply computing both whole suitable chosen level. whenever reference some atoms not available, they purposely employing reasonable computer resources. Therefore, new DFT-cost tool now characterization experiment-oriented scientists.

Language: Английский

---

Accurate Vibrational and Ro-Vibrational Contributions to the Properties of Large Molecules by a New Engine Employing Curvilinear Internal Coordinates and Vibrational Perturbation Theory to Second Order

Journal of Chemical Theory and Computation, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 31, 2024

The unbiased comparison between theory and experiment requires approaches more sophisticated than the basic harmonic-oscillator rigid-rotor model, for taking into account vibrational averaging effects ro-vibrational couplings in molecules of increasing size. Second-order perturbation based on curvilinear internal coordinates (ICs) offers a remarkable compromise accuracy computational cost, thanks to reduction mode–mode with respect their counterparts Cartesian coordinates. Therefore, we have developed, implemented, validated general engine employing ICs, which allows accurate evaluation averages containing up about 50 atoms beyond harmonic approximation. After validation new tool relatively small molecules, effectiveness ICs has been demonstrated some flexible and/or quite large molecular bricks life.

Language: Английский

---

The Semiexperimental Approach at Work: Equilibrium Structure of Radical Species

The Journal of Physical Chemistry A, Journal Year: 2024, Volume and Issue: 128(29), P. 5833 - 5855

Published: July 11, 2024

The so-called semiexperimental (SE) approach is a powerful technique for obtaining highly accurate equilibrium structures isolated systems. This Featured Article describes its extension to open-shell species, thus providing the first systematic investigation on radical geometries be used benchmarking purposes. small yet significant database obtained demonstrates that there no reduction in accuracy when moving from closed-shell species radicals. We also provide an of applicability SE medium-/large-sized radicals by exploiting "Lego-brick" approach, which based assumption molecular system can seen as formed smaller fragments structure available. In this we show model successfully applied species.

Language: Английский

---

Accurate structures and rotational constants of nitroaromatic explosives and their taggants at DFT cost by pisa composite schemes and vibrational perturbation theory

Chemical Physics Letters, Journal Year: 2025, Volume and Issue: unknown, P. 141956 - 141956

Published: Feb. 1, 2025

Language: Английский

---

Accurate Structures and Spectroscopic Parameters of CN-Substituted Polycyclic Hydrocarbons at DFT Cost

The Journal of Physical Chemistry A, Journal Year: 2025, Volume and Issue: unknown

Published: March 17, 2025

The structures, isomerization energies, and rotational vibrational spectra of prototypical CN-substituted polycyclic hydrocarbons in the gas phase have been analyzed using a general computational strategy based on Pisa composite schemes (PCS) second-order perturbation theory (VPT2). final results obtained this way show, most cases, relative average deviations with respect to experimental constants close 0.1%, corresponding errors around 1 mÅ 0.1° for bond lengths valence angles, respectively. At same time, fundamental IR absorption bands are reproduced below 10 cm–1 without any scaling factor. In addition intrinsic interest studied molecules, work confirms that spectroscopic studies large systems can be supported by unsupervised tools couple accuracy reasonable cost.

Language: Английский

---

Molecular structures with spectroscopic accuracy at DFT cost by the templating synthon approach and the PCS141 database

The Journal of Chemical Physics, Journal Year: 2025, Volume and Issue: 162(11)

Published: March 20, 2025

The computation of accurate geometric parameters at density functional theory cost for large molecules in the gas phase is addressed through a novel strategy that combines quantum chemical models with machine learning techniques. first key step expansion database semi-experimental equilibrium structures additional molecular geometries optimized by version 2 Pisa composite scheme. Then, templating synthon approach used to improve accuracy hybrid paired double zeta basis set, leveraging similarity cluster different environments and refine bond lengths valence angles. A set prototypical biomolecular building blocks demonstrate it possible achieve spectroscopic systems too be treated state-of-the-art wavefunction methods. In addition, freely accessible web-based tool has been developed facilitate post-processing using standard electronic structure codes, thereby providing an efficient computational study medium- large-sized molecules, also experiment-oriented researchers.

Language: Английский

---