Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2602.06753

Molecular origin of 31P-NMR chemical shifts of phosphate groups with bivalent counter ions

Leo Christanell·Karl-Jakob König·Julian Holzinger·Anne K. Schütz·Benjamin P. Fingerhut
View original source ↗Read source document ↗Export metadata ↓

Abstract

The electrostatic interactions of phosphate groups and counter ions critically affect the structure, function and reactivity of DNA or RNA. We present a joint experimental-theoretical investigation of dimethyl phosphate (DMP-) in aqueous solution, an established model system of the sugar-phosphate backbone. Utilizing 31P-NMR spectroscopy as probe of phosphate-ion association, variations of Mg2+ and Ca2+ content exhibit a systematic shielding of the 31P chemical shift (δiso(31P)) with moderate temperature dependence. Enhanced sampling molecular dynamics (MD) and ab initio (GIAO-DF-LMP2) level of theory are used to reveal the microscopic mechanism. Simulations are performed for a configurational ensemble of DMP-ion geometries and their first solvation shells, demonstrating (i) the spatial convergence of changes of the nuclear shielding constant σiso(31P), (ii) the intramolecular geometric origin of short-timescale σiso(31P) fluctuations and (iii) an average shift of σiso(31P) of about 3-5 ppm upon contact ion pair formation with Mg2+ or Ca2+ ions. A quantitative analysis of δiso(31P) for varying ion content and temperature allows us to extract the temperature-dependent fraction of the contact ion pair species, indicating that solvent separated or free ion pairs are the energetically preferred species. The results impose boundary conditions for improvements of phosphate ion force fields and establish the interactions underlying the changes of δiso(31P).

Explore related subjects

physics.chem-ph

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Leo Christanell, Karl-Jakob König, Julian Holzinger, Anne K. Schütz, Benjamin P. Fingerhut. 2026-02-06. Molecular origin of 31P-NMR chemical shifts of phosphate groups with bivalent counter ions. https://arxiv.org/abs/2602.06753

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Charge Transfer with a Spin. I: A Variational Constrained-CASSCF Framework for Investigating Charge Transfer in the Presence of Spin-Orbit Coupling

Charge transfer in open-shell molecular systems can involve a delicate interplay between charge localization, orbital relaxation, and spin-orbit coupling (SOC), particularly near ground-excited state crossings. Here, we introduce a very inexpensive variational framework for treating these effects in odd-electron systems by extending the electron/hole-transfer Dynamically-weighted State-Averaged Constrained CASSCF (eDSC/hDSC) method to include SOC. Our method incorporates the SOC Hamiltonian directly into the variational orbital optimization through complex-valued spinor orbitals, allowing orbital and spin degrees of freedom to relax self-consistently while preserving the time-reversal symmetry of doublet states. The method achieves smooth potential energy surfaces and rapid self-consistent field (SCF) convergence; moreover, from physically small to artificially large SOC strengths, the calculation can be converged to very tight thresholds across the whole potential energy surface. While the results presented here are for systems with two charge centers, as shown in the appendix, the theory is quite general and can be adapted to either a system of $N$ charge centers or a metal-molecule surface with a continuum of states, so that charge transport (and not just charge transfer) can also be studied. The approach therefore provides a route towards ab initio studies of spin-dependent charge transfer and charge transport in molecular systems with nontrivial spin degrees of freedom.

physics.chem-ph↗
arXiv2026

Charge Transfer with a Spin. II: A Framework for Diabatization which Localizes Charge and Spin

We investigate a diabatization procedure that localizes charges (in real space) and localizes spins (in spin space) for open-shell systems that exhibit charge transfer in the presence of spin-orbit coupling. The procedure is applied to a two-state crossing between pairs of Kramers-restricted doublet states (which can also be considered effectively a four-state crossing). To generate the relevant diabatic states, we employ a two-step optimization over complex-unitary rotations that sequentially maximizes dipole and spin moments through iterative Jacobi sweeps; the resulting update rules are effectively equivalent to those of approximate joint diagonalization (AJD) applied to charge and spin. The method converges rapidly and yields smooth diabatic potential energy surfaces that preserve dipole and spin properties (e.g., a smoothly varying spin quantization axis) along the reaction coordinate while maintaining time-reversal symmetry.

physics.chem-ph↗
arXiv2026

Fixed-Dimensional Latent Flow for Generating Variable-Size 3D Molecules

Molecular size is coupled to composition, structure, and function, yet most 3D molecular generators require a predefined atom count. We introduce Equivariant-Free Transformer-Autoencoded Latent Flow Matching, a two-stage framework that samples a fixed-dimensional latent vector using flow matching and uses an autoregressive Transformer to determine molecular size, atom types, coordinates, and chemical attributes. Canonical atom ordering and rigid-pose alignment enable Transformers without equivariant layers, while decoded attributes guide bond reconstruction. On PCQM4Mv2, unconditional generation yields 87.9\% unique, novel molecules passing sanitization and PoseBusters checks, exceeding baselines with lower end-to-end training and sampling time and higher end-to-end throughput. Across ten target HOMO-LUMO gaps, internal ranking retains 30\% of screened candidates and increases the density functional theory-verified hit rate within 0.1 eV from 25.0\% to 52.4\%, while largely preserving novelty and diversity. These results demonstrate fixed-dimensional latent generation with autoregressive decoding as a practical approach to molecular design without prespecifying size.

physics.chem-ph↗