4.6 Article

Hunting for Complex Organic Molecules in the Interstellar Medium: The Role of Accurate Low-Cost Theoretical Geometries and Rotational Constants

Related references

Note: Only part of the references are listed.
Article Chemistry, Physical

Benchmark Structures and Conformational Landscapes of Amino Acids in the Gas Phase: A Joint Venture of Machine Learning, Quantum Chemistry, and Rotational Spectroscopy

Vincenzo Barone et al.

Summary: The integration of high resolution spectroscopy and quantum mechanical computations can accurately characterize prototypical bricks of life. Using representative amino acids, a new computational setup rooted in quantum-chemical computations guided by machine learning tools is validated. The computed parameters closely match those detected in microwave experiments and serve as benchmarks for other methods.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2023)

Review Chemistry, Physical

Connections between the accuracy of rotational constants and equilibrium molecular structures

Cristina Puzzarini et al.

Summary: Rotational spectroscopy is the preferred technique for studying molecular structures in the gas phase. Rotational constants are strongly linked to the geometry of the molecules, making them useful for evaluating the accuracy of quantum chemical approaches. This review article discusses how the accuracy of computed equilibrium geometry can be measured by comparing rotational constants, and also explores the required accuracy for providing useful molecular structures and rotational constants. Quantum chemical methodologies for achieving 0.1% accuracy in rotational constants are reviewed, ranging from small molecules to small polycyclic aromatic hydrocarbons. This level of accuracy opens up possibilities for future applications, such as accurately characterizing non-covalent interactions in biological and technological processes.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2023)

Article Physics, Atomic, Molecular & Chemical

Improved semi-experimental equilibrium structure and high-level theoretical structures of ketene

Houston H. Smith et al.

JOURNAL OF CHEMICAL PHYSICS (2023)

Article Chemistry, Physical

Toward Spectroscopic Accuracy for the Structures of Large Molecules at DFT Cost: Refinement and Extension of the Nano-LEGO Approach

Vincenzo Barone et al.

Summary: The SE100 database has been extended to include species containing Br and I atoms, providing accurate equilibrium geometries of medium size molecules obtained by the semiexperimental approach. An improved Nano-LEGO tool has been developed, which offers geometrical parameters on par with state-of-the-art composite wave function methods.

JOURNAL OF PHYSICAL CHEMISTRY A (2023)

Article Chemistry, Physical

Accurate Structures and Spectroscopic Parameters of Phenylalanine and Tyrosine in the Gas Phase: A Joint Venture of DFT and Composite Wave-Function Methods

Vincenzo Barone et al.

Summary: A general strategy is utilized to accurately calculate the conformational and spectroscopic properties of phenylalanine and tyrosine, two proteinogenic amino acids with aromatic side chains, in the gas phase. The predicted stable conformers closely match those detected in microwave and infrared experiments. This accurate computation method opens up possibilities for investigating other flexible components of life.

JOURNAL OF PHYSICAL CHEMISTRY A (2023)

Article Chemistry, Physical

Accuracy Meets Feasibility for the Structures and Rotational Constants of the Molecular Bricks of Life: A Joint Venture of DFT and Wave-Function Methods

Vincenzo Barone

Summary: A fully unsupervised computational protocol is proposed to obtain reliable structural properties for molecular bricks of life in the gas phase at a moderate cost. The results of the new composite scheme approach spectroscopic accuracy without any empirical parameter, providing optimized geometries and equilibrium rotational constants. The accuracy of the new tool is comparable to state-of-the-art composite wave function methods for small semirigid molecules.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2023)

Review Chemistry, Physical

Gas-Phase Computational Spectroscopy: The Challenge of the Molecular Bricks of Life

Vincenzo Barone et al.

Summary: This review focuses on the current status and perspectives of predicting the spectral signatures of medium-sized molecules in the gas phase, with a special emphasis on rotational and vibrational spectroscopies of molecular bricks of life. It highlights the challenges posed by the scaling of quantum-chemical models with molecular size and large-amplitude internal motions.

ANNUAL REVIEW OF PHYSICAL CHEMISTRY (2023)

Article Chemistry, Physical

PCS/Bonds and PCS0: Pick your molecule and get its accurate structure and ground state rotational constants at DFT cost

Vincenzo Barone

Summary: An unsupervised computational protocol is proposed to obtain accurate structures of large molecules in the gas phase. The protocol is fully automated and provides optimized equilibrium geometries and ground state rotational constants for comparison with experiments. Results for biological or medicinal molecules show that the accuracy of the new tool is comparable to state-of-the-art composite wavefunction methods.

JOURNAL OF CHEMICAL PHYSICS (2023)

Article Chemistry, Physical

DFT Meets Wave-Function Composite Methods for Characterizing Cytosine Tautomers in the Gas Phase

Vincenzo Barone

Summary: A general strategy for accurate computation of biomolecule building blocks in gas phase, with a special focus on tautomeric equilibria, has been improved with the use of cc-pVTZ-F12 basis set, inclusion of core-valence correlation, and complete basis set extrapolation at MP2-F12 level. The resulting model chemistry is applied to cytosine tautomers and shows remarkable agreement with experimental spectroscopic parameters, enabling unbiased interpretation in terms of structure and thermochemical features. This composite method provides accurate investigations of other molecular bricks of life at reasonable cost without any empirical parameter.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2023)

Article Chemistry, Physical

Accurate Thermochemical and Kinetic Parameters at Affordable Cost by Means of the Pisa Composite Scheme (PCS)

Vincenzo Barone et al.

Summary: A new strategy for computationally studying medium-sized molecules in the gas phase is proposed in this paper, which performs better than existing model chemistries without the need for empirical parameters. The method allows nonspecialists to accurately study medium- to large-sized molecules at a reasonable cost using standard electronic structure codes.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2023)

Article Chemistry, Physical

Accurate Structures and Spectroscopic Parameters of Guanine Tautomers in the Gas Phase by the Pisa Conventional and Explicitly Correlated Composite Schemes (PCS and PCS-F12)

Vincenzo Barone et al.

Summary: A general strategy for computing the properties of biomolecule building blocks in the gas phase has been proposed and validated for tautomeric equilibria. The strategy includes core-valence correlation and wave-function composite methods with basis sets for accurate computation. The results show agreement with experimental structures and spectroscopic signatures, making it possible for non-specialists to investigate other molecular bricks of life.

JOURNAL OF PHYSICAL CHEMISTRY A (2023)

Article Chemistry, Physical

Searches for bridged bicyclic molecules in space-norbornadiene and its cyano derivatives

Marie-Aline Martin-Drumel et al.

Summary: The NBD molecule has remarkable photoswitching properties and high photostability, which make it promising for solar-thermal energy storage and a potentially important component in the interstellar medium. However, the searches for NBD, CN-NBD, and DCN-NBD in TMC-1 were unsuccessful, indicating that NBD is at least four times less abundant than indene.

FARADAY DISCUSSIONS (2023)

Article Astronomy & Astrophysics

Toward Accurate Formation Routes of Complex Organic Molecules in the Interstellar Medium: The Paradigmatic Cases of Acrylonitrile and Cyanomethanimine

Vincenzo Barone et al.

Summary: To investigate reaction mechanisms in the interstellar medium, two parameter-free model chemistries combined with double-hybrid density functionals were introduced. These methods provided accurate energies for all stationary points and were used to analyze the competition between different reaction pathways. The results revealed important reactive channels in the interstellar medium and exoplanet atmospheres.

FRONTIERS IN ASTRONOMY AND SPACE SCIENCES (2022)

Article Astronomy & Astrophysics

2021 Census of Interstellar, Circumstellar, Extragalactic, Protoplanetary Disk, and Exoplanetary Molecules

Brett A. McGuire

Summary: A total of 241 molecular species composed of 19 different elements have been detected in the interstellar and circumstellar medium through astronomical observations. These molecules vary in size from two atoms to 70 and can be detected across a wide range of wavelengths. This census provides a summary of the first detection of each molecular species, including details on the observational facility, wavelength range, transitions, and relevant laboratory spectroscopic work. Tentative and disputed detections are also listed, and tables for molecules detected in interstellar ices, external galaxies, protoplanetary disks, and exoplanetary atmospheres are included. Various visual representations of the aggregated data are briefly discussed.

ASTROPHYSICAL JOURNAL SUPPLEMENT SERIES (2022)

Article Chemistry, Physical

Accurate Quantum Chemical Spectroscopic Characterization of Glycolic Acid: A Route Toward its Astrophysical Detection

Giorgia Ceselin et al.

Summary: This study uses quantum chemical calculations to predict the structure and spectroscopic properties of glycolic acid, and provides a comparison with experimental data, enhancing the possibility of detecting this molecule.

JOURNAL OF PHYSICAL CHEMISTRY A (2022)

Article Chemistry, Physical

Steroid Hormone Androsterone Observed in the Gas Phase by Rotational Spectroscopy

Swantje V. M. Caliebe et al.

Summary: This study reports the investigation of the male sex steroid hormone androsterone in the gas phase. By combining experimental results with quantum chemical calculations, the conformation of androsterone in the gas phase was unambiguously identified.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2022)

Article Chemistry, Physical

Explicitly Correlated Double-Hybrid DFT: A Comprehensive Analysis of the Basis Set Convergence on the GMTKN55 Database

Nisha Mehta et al.

Summary: Double-hybrid density functional theory (DHDFT) offers a pathway to accuracy approaching composite wavefunction approaches such as G4 theory. By introducing F12 explicit correlation, basis set convergence of DHDFs can be greatly accelerated. The study shows that F12 significantly accelerates the basis set convergence of DHDFs, making them closer to the basis set limit in large and chemically diverse systems.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2022)

Article Astronomy & Astrophysics

Rotational spectra of interstellar N- and CN-PAHs: pyrene and coronene

Akant Vats et al.

Summary: The detection of benzonitrile and cyano-naphthalene in the cold, dark molecular cloud TMC-1 has opened up possibilities for the detection of other N- and CN-containing polycyclic aromatic hydrocarbons (PAHs). This study presents the rotational spectra of N-pyrene, CN-pyrene, N-coronene, and CN-coronene for the first time. The density functional theory calculations achieved the best performance in determining the spectroscopic parameters and simulating the rotational spectra. The large permanent dipole moment of CN-PAHs makes them suitable for detection in the interstellar medium, and CN-pyrene is a potential candidate to be discovered in cold, dark molecular clouds. This work provides a benchmark for the theoretical rotational spectra of N- and CN-containing PAHs and can guide laboratory experiments and observational searches.

MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY (2022)

Article Chemistry, Physical

Exploiting the Lego brick approach to predict accurate molecular structures of PAHs and PANHs

Hexu Ye et al.

Summary: This study utilizes the Lego brick approach to accurately determine the rotational constants of PAHs and PANHs, which are important species in space. The approach treats the molecular system as smaller fragments with known equilibrium structures and uses a template molecule approach and linear regression model to account for modifications and correct the linkage between fragments. The results demonstrate that the Lego brick approach can provide rotational constants with high relative accuracy, making it a valuable tool for predicting systems without spectroscopic characterization.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2022)

Article Astronomy & Astrophysics

Accuracy and Reliability in the Simulation of Vibrational Spectra: A Comprehensive Benchmark of Energies and Intensities Issuing From Generalized Vibrational Perturbation Theory to Second Order (GVPT2)

Qin Yang et al.

Summary: Vibrational spectroscopy is crucial for identifying and characterizing molecular species in astrochemistry and astrobiology. Computational spectroscopy, particularly DFT and VPT2 theory, play a key role in deepening our understanding, but striking a balance between reliability, feasibility, and interpretability remains a challenge.

FRONTIERS IN ASTRONOMY AND SPACE SCIENCES (2021)

Article Chemistry, Physical

Accurate Biomolecular Structures by the Nano-LEGO Approach: Pick the Bricks and Build Your Geometry

Giorgia Ceselin et al.

Summary: Accurately determining equilibrium molecular structures is crucial for understanding molecular properties, with quantum chemical computations providing precise results for small molecules and more effective approaches needed for larger ones. The SE100 database now includes important fragments containing various atoms. Linear regression can improve geometries optimized by PW6B95 and rev-DSDPBEP86 functionals, paving the way for accurate structures of large molecules with small deviations between computed and experimental results. The nano-LEGO tool has been developed to implement this approach and applied to challenging case studies.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

Article Chemistry, Physical

junChS and junChS-F12 Models: Parameter-free Efficient yet Accurate Composite Schemes for Energies and Structures of Noncovalent Complexes

Jacopo Lupi et al.

Summary: The recently developed junChS-F12 model, extended to employ F12 methods, can compute accurate interaction energies of molecular complexes without requiring empirical parameters. Performance benchmarks showed that adding MP2-F12 core-valence correlation corrections to jun-cc-pVTZ geometries is the most effective option.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

Article Chemistry, Physical

Exploring the Maze of Cycloserine Conformers in the Gas Phase Guided by Microwave Spectroscopy and Quantum Chemistry

Elena R. Alonso et al.

Summary: Cycloserine and isoxazolidine share a saturated five-membered ring structure, which is crucial for drug design and shows diverse biological activities. The most significant feature of these compounds is the N-O bond in a cyclic structure. Quantum chemical studies of cycloserine revealed multiple local energy minima, with only two separated by significant barriers, a result confirmed by experimental laser ablation microwave spectroscopy.

JOURNAL OF PHYSICAL CHEMISTRY A (2021)

Article Chemistry, Physical

Unveiling Bifunctional Hydrogen Bonding with the Help of Quantum Chemistry: The Imidazole-Water Adduct as Test Case

Alessio Melli et al.

Summary: This study accurately determined the equilibrium structure of imidazole-water complexes by combining semiexperimental methods with a template model protocol, demonstrating the reliability of the approach. The structural and energetic characteristics of the complexes were examined in detail and compared with similar adducts.

JOURNAL OF PHYSICAL CHEMISTRY A (2021)

Article Multidisciplinary Sciences

Detection of two interstellar polycyclic aromatic hydrocarbons via spectral matched filtering

Brett A. McGuire et al.

Summary: The study detected two nitrile-group-functionalized PAHs in the interstellar medium, expanding knowledge of these molecules. The paper discusses potential pathways for gas-phase PAH formation from smaller organic precursor molecules.

SCIENCE (2021)

Article Chemistry, Physical

Precise equilibrium structure determination of thiophene (c-C4H4S) by rotational spectroscopy-Structure of a five-membered heterocycle containing a third-row atom

Vanessa L. Orr et al.

Summary: The rotational spectrum of thiophene was studied and various deuterium-substituted isotopologues were synthesized to obtain precise structural parameters using computational work. The discrepancies between calculated parameters and experimental results were discussed by comparing the results with statistical limits.

JOURNAL OF CHEMICAL PHYSICS (2021)

Article Chemistry, Physical

Development and Validation of a Parameter-Free Model Chemistry for the Computation of Reliable Reaction Rates

Vincenzo Barone et al.

Summary: The recently developed jun-Cheap model chemistry is proposed as an effective, reliable, and parameter-free scheme for computing accurate reaction rates, particularly for astrochemical and atmospheric processes. Benchmarks with different energy barriers show that the proposed model outperforms well-known model chemistries in the absence of strong multireference contributions, achieving subchemical accuracy without empirical parameters and with affordable computer times. Test cases demonstrate that the geometries, energy barriers, zero point energies, and thermal contributions computed at this level can be used to obtain accurate reaction rates within the framework of the master equation approach based on ab initio transition-state theory.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

Article Multidisciplinary Sciences

Detection of two interstellar polycyclic aromatic hydrocarbons via spectral matched filtering

Brett A. McGuire et al.

Summary: Unidentified infrared emission bands are commonly attributed to PAH molecules, and in this study, two nitrile-group-functionalized PAHs were detected in the interstellar medium. The study also discusses potential pathways for gas-phase PAH formation from smaller organic precursor molecules.

SCIENCE (2021)

Article Chemistry, Physical

Extension of the Cheap Composite Approach to Noncovalent Interactions: The jun-ChS Scheme

Silvia Alessandrini et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Review Astronomy & Astrophysics

Spitzer's perspective of polycyclic aromatic hydrocarbons in galaxies

Aigen Li

NATURE ASTRONOMY (2020)

Article Chemistry, Physical

How Accurate Is Density Functional Theory at Predicting Dipole Moments? An Assessment Using a New Database of 200 Benchmark Values

Diptarka Hait et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

Article Physics, Atomic, Molecular & Chemical

The equilibrium structure of hydrogen peroxide

Joshua H. Baraban et al.

JOURNAL OF MOLECULAR SPECTROSCOPY (2018)

Article Multidisciplinary Sciences

Detection of the aromatic molecule benzonitrile (c-C6H5CN) in the interstellar medium

Brett A. McGuire et al.

SCIENCE (2018)

Review Chemistry, Multidisciplinary

A computational chemist's guide to accurate thermochemistry for organic molecules

Amir Karton

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2016)

Article Chemistry, Physical

Semiexperimental Equilibrium Structures for Building Blocks of Organic and Biological Molecules: The B2PLYP Route

Emanuele Penocchio et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Multidisciplinary

All Five Forms of Cytosine Revealed in the Gas Phase

Jose L. Alonso et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2013)

Article Chemistry, Physical

Electronic, vibrational, and rotational structures in the S0 1A1 and S1 1A1 states of phenanthrene

Yasuyuki Kowaka et al.

JOURNAL OF CHEMICAL PHYSICS (2012)

Article Chemistry, Physical

Perspectives on Basis Sets Beautiful: Seasonal Plantings of Diffuse Basis Functions

Ewa Papajak et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

Review Chemistry, Physical

Quantum-chemical calculation of spectroscopic parameters for rotational spectroscopy

Cristina Puzzarini et al.

INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY (2010)

Article Chemistry, Physical

Extrapolation to the Complete Basis Set Limit of Structural Parameters: Comparison of Different Approaches

Cristina Puzzarini

JOURNAL OF PHYSICAL CHEMISTRY A (2009)

Article Chemistry, Inorganic & Nuclear

Covalent radii revisited

Beatriz Cordero et al.

DALTON TRANSACTIONS (2008)

Article Chemistry, Physical

Systematically convergent basis sets for explicitly correlated wavefunctions: The atoms H, He, B-Ne, and Al-Ar

Kirk A. Peterson et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Astronomy & Astrophysics

Rotational spectra of small PAHs:: Acenaphthene, acenaphthylene, azulene, and fluorene

S. Thorwirth et al.

ASTROPHYSICAL JOURNAL (2007)

Article Chemistry, Physical

Anharmonic vibrational properties by a fully automated second-order perturbative approach

V Barone

JOURNAL OF CHEMICAL PHYSICS (2005)

Article Chemistry, Multidisciplinary

Conformational preferences of jet-cooled melatonin:: Probing trans- and cis-amide regions of the potential energy surface

GM Florio et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)