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Abstract Background Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. Results Testing of newly developed markers on a set of 36 Lactuca accession (33 L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe = 0.56) and the number of loci per SSR (Na = 5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe = 0.32, Na = 3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. Conclusions The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping of genes.

Abstract Background Lettuce (Lactuca saliva L.) is susceptible to dieback, a soilborne disease caused by two viruses from the family Tombusviridae. Susceptibility to dieback is widespread in romaine and leaf-type lettuce, while modern iceberg cultivars are resistant to this disease. Resistance in iceberg cultivars is conferred by Tvr1 - a single, dominant gene that provides durable resistance. This study describes fine mapping of the resistance gene, analysis of nucleotide polymorphism and linkage disequilibrium in the Tvr1 region, and development of molecular markers for marker-assisted selection. Results A combination of classical linkage mapping and association mapping allowed us to pinpoint the location of the Tvr1 resistance gene on chromosomal linkage group 2. Nine molecular markers, based on expressed sequence tags (EST), were closely linked to Tvr1 in the mapping population, developed from crosses between resistant (Salinas and Salinas 88) and susceptible (Valmaine) cultivars. Sequencing of these markers from a set of 68 cultivars revealed a relatively high level of nucleotide polymorphism (θ = 6.7 × 10-3) and extensive linkage disequilibrium (r2 = 0.124 at 8 cM) in this region. However, the extent of linkage disequilibrium was affected by population structure and the values were substantially larger when the analysis was performed only for romaine (r2 = 0.247) and crisphead (r2 = 0.345) accessions. The association mapping approach revealed that one of the nine markers (Cntg10192) in the Tvr1 region matched exactly with resistant and susceptible phenotypes when tested on a set of 200 L. sativa accessions from all horticultural types of lettuce. The marker-trait association was also confirmed on two accessions of Lactuca serriola - a wild relative of cultivated lettuce. The combination of three single-nucleotide polymorphisms (SNPs) at the Cntg10192 marker identified four haplotypes. Three of the haplotypes were associated with resistance and one of them was always associated with susceptibility to the disease. Conclusion We have successfully applied high-resolution DNA melting (HRM) analysis to distinguish all four haplotypes of the Cntg10192 marker in a single analysis. Marker-assisted selection for dieback resistance with HRM is now an integral part of our breeding program that is focused on the development of improved lettuce cultivars.

The water trimer, as the smallest water cluster in which the three-body interactions can manifest, is arguably the most important hydrogen-bonded trimer. Accurate, fully coupled quantum treatment of its excited intermolecular vibrations has long been an elusive goal. Here, we present the methodology that for the first time allows rigorous twelve-dimensional (12D) quantum calculation of the intermolecular vibration-tunneling eigenstates of the water trimer, with the monomers treated as rigid. These 12D eigenstates are used to simulate the low-frequency absorption spectrum of the trimer for direct comparison with the measured far-infrared (FIR) spectrum of the water trimer in helium nanodroplets. The 12D calculations reveal weak coupling between the large-amplitude torsional and intermolecular stretching vibrations. The calculated torsional tunneling splittings are in excellent agreement with spectroscopic results. There are visible differences between the spectrum simulated using the 12D eigenstates and that based on our earlier 9D calculations where the stretching vibrations are not included. The peaks in the 12D spectrum are generally shifted to slightly lower energies relative to those in the 9D spectrum, as well as the measured FIR spectrum, and are often split by intermolecular stretch-bend Fermi resonances that the 9D treatment cannot capture., (© 2025 Author(s). Published under an exclusive license by AIP Publishing.)

We present the computational methodology that enables the first rigorous nine-dimensional (9D) quantum calculations of the intermolecular bending states of the water trimer, as well as its low-frequency spectrum for direct comparison with experiment. The water monomers, treated as rigid, have their centers of mass (cm's) at the corners of an equilateral triangle, and the intermonomer cm-to-cm distance is set to a value slightly larger than that in the equilibrium geometry of the trimer. The remaining nine strongly coupled large-amplitude bending (angular) degrees of freedom (DOFs) enter the 9D bend Hamiltonian of the three coupled 3D rigid-water hindered rotors. Its 9D eigenstates encompass excited librational vibrations of the trimer, as well as their torsional and bifurcation tunneling splittings, which have been the subject of much interest. The calculations of these eigenstates are extremely demanding, and a sophisticated computational scheme is developed that exploits the molecular symmetry group of the water trimer, G 48 , in order to make them feasible in a reasonable amount of time. The spectrum of the low-frequency vibrations of the water trimer simulated using the eigenstates of the 9D bend Hamiltonian agrees remarkably well with the experimentally observed far-infrared (FIR) spectrum of the trimer in helium nanodroplets over the entire frequency range of the measurements from 70 to 620 cm -1 . This shows that most peaks in the experimental FIR spectrum are associated with the intermolecular bending vibrations of the trimer. Moreover, the ground-state torsional tunneling splittings from the present 9D calculations are in excellent agreement with the spectroscopic data. These results demonstrate the high quality of the ab initio 2 + 3-body PES employed for the DOFs included in the bound-state calculations.

We present fully coupled, full-dimensional quantum calculations of the inter- and intra-molecular vibrational states of HCl trimer, a paradigmatic hydrogen-bonded molecular trimer. They are performed utilizing the recently developed methodology for the rigorous 12D quantum treatment of the vibrations of the noncovalently bound trimers of flexible diatomic molecules [Felker and Bačić, J. Chem. Phys. 158, 234109 (2023)], which was previously applied to the HF trimer by us. In this work, the many-body 12D potential energy surface (PES) of (HCl)3 [Mancini and Bowman, J. Phys. Chem. A 118, 7367 (2014)] is employed. The calculations extend to the intramolecular HCl-stretch excited vibrational states of the trimer with one- and two-quanta, together with the low-energy intermolecular vibrational states in the two excited v = 1 intramolecular vibrational manifolds. They reveal significant coupling between the intra- and inter-molecular vibrational modes. The 12D calculations also show that the frequencies of the v = 1 HCl stretching states of the HCl trimer are significantly redshifted relative to those of the isolated HCl monomer. Detailed comparison is made between the results of the 12D calculations on the two-body PES, obtained by removing the three-body term from the original 2 + 3-body PES, and those computed on the 2 + 3-body PES. It demonstrates that the three-body interactions have a strong effect on the trimer binding energy as well as on its intra- and inter-molecular vibrational energy levels. Comparison with the available spectroscopic data shows that good agreement with the experiment is achieved only if the three-body interactions are included. Some low-energy vibrational states localized in a secondary minimum of the PES are characterized as well., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Detailed structural, dynamical, and vibrational analyses have been performed for systems composed of linear triatomic molecules solvated by a single rare-gas atom, He, Ne, or Ar. Among the chromophores of these van der Waals (vdW) dimers, there are four neutral molecules (CO 2 , CS 2 , N 2 O, and OCS) and six molecular cations (HHe 2 + , HNe 2 + , HAr 2 + , HHeNe + , HHeAr + , and HNeAr + ), both of apolar and polar nature. Following the exploration of bonding preferences, high-level four-dimensional (4D) potential energy surfaces (PESs) have been developed for 24 vdW dimers, keeping the two intramonomer bond lengths fixed. For these 24 complexes, over 1500 bound vibrational states have been obtained via quasi-variational nuclear-motion computations, employing exact kinetic-energy operators together with the accurate 4D PESs and their 2D/3D cuts. The reduced-dimensional (2D to 4D) dimer models have been compared with full-dimensional (6D) ones in the cases of the neutral CO 2 ·Ar and charged HHe 2 + ·He dimers, corroborating the high accuracy of the 2D to 4D vibrational energies. The reduced-dimensional models suggest that (a) while the equilibrium structures are T-shaped and planar, the effective ground-state structures are nonplanar, (b) certain bound states belong to collinear molecular structures, even when they are not minima, (c) the vdW vibrations are heavily mixed and many states have amplitudes corresponding to both the T-shaped and collinear structures, (d) there are a few dimers, for which even some of the vdW fundamentals lie above the first dissociation limit, and (e) the vdW vibrations are almost fully decoupled from the intramonomer bending motion.

Intramolecular vibrational transition wavenumbers and intensities were calculated in the fundamental HOH-bending, fundamental OH-stretching, first OH-stretching-HOH-bending combination, and first OH-stretching overtone (Δ v OH = 2) regions of the water dimer's spectrum. Furthermore, the rotational-vibrational spectrum was calculated in the Δ v OH = 2 region at 10 K, corresponding to the temperature of the existing jet-expansion experiments. The calculated spectrum was obtained by combining results from a full-dimensional (12D) vibrational and a reduced-dimensional vibrational-rotational-tunneling model. The Δ v OH = 2 spectral region is rich in features due to contributions from multiple vibrational-rotational-tunneling sub-bands. Origins of the experimental vibrational bands depend on the assignment of the observed sub-bands. Based on our calculations, we assign the observed sub-bands, and our reassignment leads to new values for the vibrational band origins of the free donor and antisymmetric acceptor OH-stretching first overtones of ∼7227 and ∼7238 cm -1 , respectively. The observed bands with origins at 7192.34 and ∼7366 cm -1 are assigned to the symmetric acceptor OH-stretching first overtone and the OH-stretching combination of the donor, respectively.

Experimental and computational results about the structure, dynamics, and rovibrational spectra of protonated methane have challenged a considerable number of traditional chemical concepts. Hereby theoretical and computational results are provided about the dynamical structure of CH 5 + . It is shown that the ground vibrational state investigated thus far by computations, forbidden by nuclear-spin statistics, has a structure similar to the first allowed vibrational state and, in fact, the structures of all vibrational states significantly below 200 cm -1 are highly similar. Spatial delocalization of the nuclei, determined by nuclear densities computed from accurate variational vibrational wave functions, turns out to be limited when viewed in the body-fixed frame, confirming that the effective structure of CH 5 + is well described as a CH 3 + tripod with a H 2 unit on top of it. The interesting and unusual qualitative aspects of the sophisticated state-dependent variational results receive full explanation via simple quantum-graph models.

Increasing interest in the fields of high-harmonics generation, laser-induced chemical reactions, and molecular imaging of gaseous targets demands high molecular "alignment" and "orientation" (A&O). In this work, we examine the critical role of different pulse parameters on the field-free A&O dynamics of the CH[Formula: see text]F molecule, and identify experimentally feasible optical and THz range laser parameters that ensure maximal A&O for such molecules. Herein, apart from rotational temperature, we investigate effects of varying pulse parameters such as, pulse duration, intensity, frequency, and carrier envelop phase (CEP). By analyzing the interplay between laser pulse parameters and the resulting rotational population distribution, the origin of specific A&O dynamics was addressed. We could identify two qualitatively different A&O behaviors and revealed their connection with the pulse parameters and the population of excited rotational states. We report here the highest alignment of [Formula: see text] and orientation of [Formula: see text] for CH[Formula: see text]F molecule at 2 K using a single pulse. Our study should be useful to understand different aspects of laser-induced unidirectional rotation in heteronuclear molecules, and in understanding routes to tune/enhance A&O in laboratory conditions for advanced applications., (© 2022. The Author(s).)

A model based on the finite-basis representation of a vibrational Hamiltonian expressed in internal coordinates is developed. The model relies on a many-mode, low-order expansion of both the kinetic energy operator and the potential energy surface (PES). Polyad truncations and energy ceilings are used to control the size of the vibrational basis to facilitate accurate computations of the OH stretch and HOH bend intramolecular transitions of the water dimer (H 2 16 O) 2 . Advantages and potential pitfalls of the applied approximations are highlighted. The importance of choices related to the treatment of the kinetic energy operator in reduced-dimensional calculations and the accuracy of different water dimer PESs are discussed. A range of different reduced-dimensional computations are performed to investigate the wavenumber shifts in the intramolecular transitions caused by the coupling between the intra- and intermolecular modes. With the use of symmetry, full 12-dimensional vibrational energy levels of the water dimer are calculated, predicting accurately the experimentally observed intramolecular fundamentals. It is found that one can also predict accurate intramolecular transition wavenumbers for the water dimer by combining a set of computationally inexpensive reduced-dimensional calculations, thereby guiding future effective-Hamiltonian treatments.

Motivated by recent experiments, the laser-induced alignment-and-orientation (A&O) dynamics of the prolate symmetric top CH 3 X (X = F, Cl, Br, I) molecules is investigated, with particular emphasis on the effect of halogen substitution on the rotational constants, dipole moments, and polarizabilities of these species, as these quantities determine the A&O dynamics. Insight into possible control schemes for preferred A&O dynamics of halogenated molecules and best practices for A&O simulations are provided, as well. It is shown that for accurate A&O -dynamics simulations it is necessary to employ large basis sets and high levels of electron correlation when computing the rotational constants, dipole moments, and polarizabilities. The benchmark-quality values of these molecular parameters, corresponding to the equilibrium, as well as the vibrationally averaged structures are obtained with the help of the focal-point analysis (FPA) technique and explicit electronic-structure computations utilizing the gold-standard CCSD(T) approach, basis sets up to quintuple-zeta quality, core-correlation contributions and, in particular, relativistic effects for CH 3 Br and CH 3 I. It is shown that the different A&O behavior of the CH 3 X molecules in the optical regime is mostly caused by the differences in their polarizability anisotropy, in other terms, the size of the halogen atom. In contrast, the A&O dynamics of the CH 3 X series induced by an intense few-cycle THz pulse is mostly governed by changes in the rotational constants, due to the similar dipole moments of the CH 3 X molecules. The A&O dynamics is most sensitive to the B rotational constant: even the difference between its equilibrium and vibrationally-averaged values results in noticeably different A&O dynamics. The contribution of rotational states having different symmetry, weighted by nuclear-spin statistics, to the A&O dynamics is also studied., (© 2022 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC.)

Resonance states are characterized by an energy that is above the lowest dissociation threshold of the potential energy hypersurface of the system and thus resonances have finite lifetimes. All molecules possess a large number of long- and short-lived resonance (quasibound) states. A considerable number of rotational-vibrational resonance states are accessible not only via quantum-chemical computations but also by spectroscopic and scattering experiments. In a number of chemical applications, most prominently in spectroscopy and reaction dynamics, consideration of rotational-vibrational resonance states is becoming more and more common. There are different first-principles techniques to compute and rationalize rotational-vibrational resonance states: one can perform scattering calculations or one can arrive at rovibrational resonances using variational or variational-like techniques based on methods developed for determining bound eigenstates. The latter approaches can be based either on the Hermitian (L 2 , square integrable) or non-Hermitian (non-L 2 ) formalisms of quantum mechanics. This Perspective reviews the basic concepts related to and the relevance of shape and Feshbach-type rotational-vibrational resonance states, discusses theoretical methods and computational tools allowing their efficient determination, and shows numerical examples from the authors' previous studies on the identification and characterization of rotational-vibrational resonances of polyatomic molecular systems.

Frequency combs and cavity-enhanced optical techniques have revolutionized molecular spectroscopy: their combination allows recording saturated Doppler-free lines with ultrahigh precision. Network theory, based on the generalized Ritz principle, offers a powerful tool for the intelligent design and validation of such precision-spectroscopy experiments and the subsequent derivation of accurate energy differences. As a proof of concept, 156 carefully-selected near-infrared transitions are detected for H 2 16 O, a benchmark system of molecular spectroscopy, at kHz accuracy. These measurements, augmented with 28 extremely-accurate literature lines to ensure overall connectivity, allow the precise determination of the lowest ortho-H 2 16 O energy, now set at 23.794 361 22(25) cm -1 , and 160 energy levels with similarly high accuracy. Based on the limited number of observed transitions, 1219 calibration-quality lines are obtained in a wide wavenumber interval, which can be used to improve spectroscopic databases and applied to frequency metrology, astrophysics, atmospheric sensing, and combustion chemistry.

A general and semi-automatic technique, based on the complex absorbing potential (CAP) method, is developed for the variational computation and identification of rotational-vibrational resonance states. This technique is an extension of a method introduced by Tremblay and Carrington ( J. Chem. Phys. 2005, 122, 244107 ), and it employs the damped eigenvectors of a CAP-modified Hamiltonian as a basis to describe resonance wave functions. The low-lying resonances of the weakly bound Ar·NO + complex are computed with the new and the traditional CAP techniques to test the new algorithm. As an additional, more challenging test case, the bound and resonance rovibrational states of the H 2 dimer, the latter with both negative and positive binding energies, are determined, corresponding to different rotational excitations of the H 2 monomers. Resonances above the first few dissociation channels of (H 2 ) 2 are computed with the new and the traditional CAP methods, revealing some new, assigned resonance quantum states not reported in the literature.