Exploring the Maze of Cycloserine Conformers in the Gas Phase Guided by Microwave Spectroscopy and Quantum Chemistry
04 Mar 2021-Journal of Physical Chemistry A (American Chemical Society (ACS))-Vol. 125, Iss: 10, pp 2121-2129
TL;DR: In this article, a detailed characterization of cycloserine and isoxazolidine has been presented, showing that the rev-DSD-PBEP86 functional is competitive with respect to explicitly correlated coupled-cluster computations.
Abstract: Cycloserine has in common with isoxazolidines the saturated five-membered ring, which is an important scaffold for drug design, exhibiting diverse biological activities. The most remarkable feature of these compounds is the presence of the N-O bond framed in a cyclic moiety. The lack of an accurate characterization of this structural feature in an isolated system calls for a state-of-the-art theoretical-experimental study. A quantum-chemical investigation of cycloserine unveiled the presence of 11 local energy minima, with only two of them being separated by significant barriers. This picture has been experimentally confirmed: two species have been unequivocally detected in the gas phase by means of laser ablation microwave spectroscopy, also disentangling the complicated hyperfine structure originating from the presence of two nitrogen atoms. A thorough characterization of cycloserine and isoxazolidine, benchmarked by the semiexperimental investigation of hydroxylamine, provided the first accurate determination of their structures and pointed out that the rev-DSD-PBEP86 functional is competitive with respect to explicitly correlated coupled-cluster computations. This outcome paves the way toward accurate studies of large flexible molecules.
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TL;DR: In this paper, a recently developed model chemistry (jun-cheap) has been modified and proposed as an effective, reliable, and parameter-free scheme for the computation of accurate reaction rates with special reference to astrochemical and atmospheric processes.
Abstract: A recently developed model chemistry (jun-Cheap) has been slightly modified and proposed as an effective, reliable, and parameter-free scheme for the computation of accurate reaction rates with special reference to astrochemical and atmospheric processes. Benchmarks with different sets of state-of-the-art energy barriers spanning a wide range of values show that, in the absence of strong multireference contributions, the proposed model outperforms the most well-known model chemistries, reaching a subchemical accuracy without any empirical parameter and with affordable computer times. Some test cases show that geometries, energy barriers, zero point energies, and thermal contributions computed at this level can be used in the framework of the master equation approach based on the ab initio transition-state theory for obtaining accurate reaction rates.
21 citations
TL;DR: In this paper, a family of effective, reliable, and parameter-free schemes for the computation of accurate interaction energies of molecular complexes ruled by noncovalent interactions is proposed, which employs cost-effective revDSD-PBEP86-D3(BJ) reference geometries.
Abstract: A recently developed model chemistry (denoted as junChS [Alessandrini, S.; et al. J. Chem. Theory Comput.2020,16, 988-1006]) has been extended to the employment of explicitly correlated (F12) methods. This led us to propose a family of effective, reliable, and parameter-free schemes for the computation of accurate interaction energies of molecular complexes ruled by noncovalent interactions. A thorough benchmark based on a wide range of interactions showed that the so-called junChS-F12 model, which employs cost-effective revDSD-PBEP86-D3(BJ) reference geometries, has an improved performance with respect to its conventional counterpart and outperforms well-known model chemistries. Without employing any empirical parameter and at an affordable computational cost, junChS-F12 reaches subchemical accuracy. Accurate characterizations of molecular complexes are usually limited to energetics. To take a step forward, the conventional and F12 composite schemes developed for interaction energies have been extended to structural determinations. A benchmark study demonstrated that the most effective option is to add MP2-F12 core-valence correlation corrections to fc-CCSD(T)-F12/jun-cc-pVTZ geometries without the need of recovering the basis set superposition error and the extrapolation to the complete basis set.
16 citations
TL;DR: In this article, the authors describe new perspectives for computational spectroscopy, in the framework of a strategy in which computational methodologies at the state of the art, high-performance computing, artificial intelligence and virtual reality tools are integrated with the aim of improving research throughput and achieving goals otherwise not possible.
Abstract: The established pillars of computational spectroscopy are theory and computer based simulations. Recently, artificial intelligence and virtual reality are becoming the third and fourth pillars of an integrated strategy for the investigation of complex phenomena. The main goal of the present contribution is the description of some new perspectives for computational spectroscopy, in the framework of a strategy in which computational methodologies at the state of the art, high-performance computing, artificial intelligence and virtual reality tools are integrated with the aim of improving research throughput and achieving goals otherwise not possible. Some of the key tools (e.g., continuous molecular perception model and virtual multifrequency spectrometer) and theoretical developments (e.g., non-periodic boundaries, joint variational-perturbative models) are shortly sketched and their application illustrated by means of representative case studies taken from recent work by the authors. Some of the results presented are already well beyond the state of the art in the field of computational spectroscopy, thereby also providing a proof of concept for other research fields.
12 citations
TL;DR: In this paper , a new computational setup rooted in quantum-chemical computations of increasing accuracy guided by machine learning tools is proposed to validate a new set of representative amino acids (glycine, alanine, serine, cysteine, threonine, aspartic acid and asparagine).
Abstract: The accurate characterization of prototypical bricks of life can strongly benefit from the integration of high resolution spectroscopy and quantum mechanical computations. We have selected a number of representative amino acids (glycine, alanine, serine, cysteine, threonine, aspartic acid and asparagine) to validate a new computational setup rooted in quantum-chemical computations of increasing accuracy guided by machine learning tools. Together with low-lying energy minima, the barriers ruling their interconversion are evaluated in order to unravel possible fast relaxation paths. Vibrational and thermal effects are also included in order to estimate relative free energies at the temperature of interest in the experiment. The spectroscopic parameters of all the most stable conformers predicted by this computational strategy, which do not have low-energy relaxation paths available, closely match those of the species detected in microwave experiments. Together with their intrinsic interest, these accurate results represent ideal benchmarks for more approximate methods.
6 citations
TL;DR: In this paper, the structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster theory.
Abstract: The structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap" composite approach (CCSD(T)/(CBS+CV)MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm-1, has been obtained by combining CCSD(T)/(CBS+CV)MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included.
5 citations
References
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TL;DR: This work reports a gradient-corrected exchange-energy functional, containing only one parameter, that fits the exact Hartree-Fock exchange energies of a wide variety of atomic systems with remarkable accuracy, surpassing the performance of previous functionals containing two parameters or more.
Abstract: Current gradient-corrected density-functional approximations for the exchange energies of atomic and molecular systems fail to reproduce the correct 1/r asymptotic behavior of the exchange-energy density. Here we report a gradient-corrected exchange-energy functional with the proper asymptotic limit. Our functional, containing only one parameter, fits the exact Hartree-Fock exchange energies of a wide variety of atomic systems with remarkable accuracy, surpassing the performance of previous functionals containing two parameters or more.
45,683 citations
TL;DR: In this paper, a detailed study of correlation effects in the oxygen atom was conducted, and it was shown that primitive basis sets of primitive Gaussian functions effectively and efficiently describe correlation effects.
Abstract: In the past, basis sets for use in correlated molecular calculations have largely been taken from single configuration calculations. Recently, Almlof, Taylor, and co‐workers have found that basis sets of natural orbitals derived from correlated atomic calculations (ANOs) provide an excellent description of molecular correlation effects. We report here a careful study of correlation effects in the oxygen atom, establishing that compact sets of primitive Gaussian functions effectively and efficiently describe correlation effects i f the exponents of the functions are optimized in atomic correlated calculations, although the primitive (s p) functions for describing correlation effects can be taken from atomic Hartree–Fock calculations i f the appropriate primitive set is used. Test calculations on oxygen‐containing molecules indicate that these primitive basis sets describe molecular correlation effects as well as the ANO sets of Almlof and Taylor. Guided by the calculations on oxygen, basis sets for use in correlated atomic and molecular calculations were developed for all of the first row atoms from boron through neon and for hydrogen. As in the oxygen atom calculations, it was found that the incremental energy lowerings due to the addition of correlating functions fall into distinct groups. This leads to the concept of c o r r e l a t i o n c o n s i s t e n t b a s i s s e t s, i.e., sets which include all functions in a given group as well as all functions in any higher groups. Correlation consistent sets are given for all of the atoms considered. The most accurate sets determined in this way, [5s4p3d2f1g], consistently yield 99% of the correlation energy obtained with the corresponding ANO sets, even though the latter contains 50% more primitive functions and twice as many primitive polarization functions. It is estimated that this set yields 94%–97% of the total (HF+1+2) correlation energy for the atoms neon through boron.
26,705 citations
TL;DR: It is shown by an extensive benchmark on molecular energy data that the mathematical form of the damping function in DFT‐D methods has only a minor impact on the quality of the results and BJ‐damping seems to provide a physically correct short‐range behavior of correlation/dispersion even with unmodified standard functionals.
Abstract: It is shown by an extensive benchmark on molecular energy data that the mathematical form of the damping function in DFT-D methods has only a minor impact on the quality of the results. For 12 different functionals, a standard "zero-damping" formula and rational damping to finite values for small interatomic distances according to Becke and Johnson (BJ-damping) has been tested. The same (DFT-D3) scheme for the computation of the dispersion coefficients is used. The BJ-damping requires one fit parameter more for each functional (three instead of two) but has the advantage of avoiding repulsive interatomic forces at shorter distances. With BJ-damping better results for nonbonded distances and more clear effects of intramolecular dispersion in four representative molecular structures are found. For the noncovalently-bonded structures in the S22 set, both schemes lead to very similar intermolecular distances. For noncovalent interaction energies BJ-damping performs slightly better but both variants can be recommended in general. The exception to this is Hartree-Fock that can be recommended only in the BJ-variant and which is then close to the accuracy of corrected GGAs for non-covalent interactions. According to the thermodynamic benchmarks BJ-damping is more accurate especially for medium-range electron correlation problems and only small and practically insignificant double-counting effects are observed. It seems to provide a physically correct short-range behavior of correlation/dispersion even with unmodified standard functionals. In any case, the differences between the two methods are much smaller than the overall dispersion effect and often also smaller than the influence of the underlying density functional.
14,151 citations
TL;DR: In this paper, a new augmented version of coupled-cluster theory, denoted as CCSD(T), is proposed to remedy some of the deficiencies of previous augmented coupledcluster models.
7,249 citations
TL;DR: In this article, a unique mean plane is defined for a general monocyclic puckered ring, which is described by amplitude and phase coordinates which are generalizations of those introduced for cyclopentane by Kilpatrick, Pitzer, and Spitzer.
Abstract: A unique mean plane is defined for a general monocyclic puckered ring. The geometry of the puckering relative to this plane is described by amplitude and phase coordinates which are generalizations of those introduced for cyclopentane by Kilpatrick, Pitzer, and Spitzer. Unlike earlier treatments based on torsion angles, no mathematical approximations are involved. A short treatment of the four-, five-, and six-membered ring demonstrates the usefulness of this concept. Finally, an example is given of the analysis of crystallographic structural data in terms of these coordinates. Although the nonplanar character of closed rings in many cyclic compounds has been widely recognized for many years, there remain some difficulties in its quantitative specification. An important first step was taken by Kilpatrick, Pitzer, and Spitzer in their 1947 discussion of the molecular structure of cyclopentane.' Starting with the normal modes of out-of-plane motions of a planar regular pentagon,* they pointed out that displacement of the j t h carbon atom perpendicular to the plane could be written 2 112 zj = (/'SI 4 COS (2+ + 4 n ( j 11/51 (11 where q is a puckering amplitude and $ is a phase angle describing various kinds of puckering. By considering changes in an empirical potential energy for displacements perpendicular to the original planar form, they gave reasons to believe that the lowest energy was obtained for a nonzero value of q (finite puckering) but that this minimum was largely independent of $. Motion involving a change in fi at constant q was described as pseudorotation. Subsequent refinement of this work has involved models in which constraints to require constant bond lengths are imposed3q4 and extensions to larger rings5-' and some heterocyclic systems are considered.* Although the correctness of the model of Kilpatrick, et a f . , I and the utility of the (q. $) coordinate system is generally accepted, application to a general five-membered ring with unequal bond lengths and angles is not straightforward. Given the Cartesian coordinates for the five atoms (as from a crystal structure), determination of puckering displacements z, requires specification of the plane z = 0. A least-squares choice (minimization of Zz i2) is one possibility, but the five displacements relative to this plane cannot generally be expressed in terms of two parameters q and $ according to eq 1. An attempt to define a generalized set of puckering cordinates which avoids these difficulties was made by Geise, Altona, Romers, and S~ndara l ingam.~l ' Their quantitative description of puckering in five-membered rings involves the five torsion angles 0, rather than displacements perpendicular to some plane. These torsion angles are directly derivable from the atomic coordinates and are all zero in the planar form. They proposed a relationship of the form\
6,526 citations