Three-dimensional models for the aqueous solvation structures of chloride, bromide, and iodide are reported. K-edge extended X-ray absorption fine structure (EXAFS) and Minuit X-ray absorption near edge (MXAN) analyses found well-defined single shell solvation spheres for bromide and iodide. However, dissolved chloride proved structurally distinct, with two solvation shells needed to explain its strikingly different X-ray absorption near edge structure (XANES) spectrum. Final solvation models were as follows: iodide, 8 water molecules at 3.60 ± 0.13 Å and bromide, 8 water molecules at 3.40 ± 0.14 Å, while chloride solvation included 7 water molecules at 3.15 ± 0.10 Å, and a second shell of 7 water molecules at 4.14 ± 0.30 Å. Each of the three derived solvation shells is approximately uniformly disposed about the halides, with no global asymmetry. Time-dependent density functional theory calculations simulating the chloride XANES spectra following from alternative solvation spheres revealed surprising sensitivity of the electronic state to 6-, 7-, or 8-coordination, implying a strongly bounded phase space for the correct structure during an MXAN fit. MXAN analysis further showed that the asymmetric solvation predicted from molecular dynamics simulations using halide polarization can play no significant part in bulk solvation. Classical molecular dynamics used to explore chloride solvation found a 7-water solvation shell at 3.12 (−0.04/+0.3) Å, supporting the experimental result. These experiments provide the first fully three-dimensional structures presenting to atomic resolution the aqueous solvation spheres of the larger halide ions.

High-resolution EXAFS (k = 18 Å⁻¹) and MXAN XAS analyses show that axially elongated square pyramidal [Cu(H₂O)₅]²⁺ dominates the structure of Cu(II) in aqueous solution, rather than 6-coordinate JT-octahedral [Cu(H₂O)₆]²⁺. Freezing produced a shoulder at 8989.6 eV on the rising XAS edge and an altered EXAFS spectrum, while 1s → 3d transitions remained invariant in energy position and intensity. Core square pyramidal [Cu(H₂O)₅]²⁺ also dominates frozen solution. Solvation shells were found at ∼3.6 Å (EXAFS) or ∼3.8 Å (MXAN) in both liquid and frozen phases. However, MXAN analysis revealed that about half the time in liquid solution, [Cu(H₂O)₅]²⁺ associates with an axially non-bonding 2.9 Å water molecule. This distant water apparently organizes the solvation shell. When the 2.9 Å water molecule is absent, the second shell is undetectable to MXAN. The two structural arrangements may represent energetic minima of fluxional dissolved aqueous [Cu(H₂O)₅]²⁺. The 2.9 Å trans-axial water resolves an apparent conflict of the [Cu(H₂O)₅]²⁺ core model with a dissociational exchange mechanism. In frozen solution, [Cu(H₂O)₅]²⁺ is associated with either a 3.0 Å axial non-bonded water molecule or an axial ClO₄⁻ at 3.2 Å. Both structures are again of approximately equal presence. When the axial ClO₄⁻ is present, Cu(II) is ∼0.5 Å above the mean O₄ plane. This study establishes [Cu(H₂O)₅]²⁺ as the dominant core structure for Cu(II) in water solution, and is the first to both empirically resolve multiple extended solution structures for fluxional [Cu(H₂O)₅]²⁺ and to provide direct evidence for second shell dynamics.

About a hundred years ago, the Russian biologist A. Gurwitsch, based on experiments with onion plants by measuring their growth rate, hypothesized that plants emit a weak electromagnetic field that somehow influences cell growth. This interesting observation remained fundamentally ignored by the scientific community; only in the 1950s the electromagnetic emission from some plants was measured using a photomultiplier used in single counting mode. Later, in the 1980s, several groups around the world started extensive work to understand the origin and role of this ultraweak emission, now called biophotons, coming from living organisms. Biophotons are an endogenous very small production of photons in the visible energy range in and from cells and organisms, and this emission is characteristic of living organisms. Today, there is no doubt that biophotons exist, this emission has been measured by many groups and for many different living organisms, from humans to bacteria. However, the origin of biophotons and whether organisms use them to exchange information is not yet well understood; no model proposed to date is capable of reproducing and interpreting the great variety of experimental data coming from the many different living systems measured so far. In this brief review, we present our experimental work on the biophotons coming from germinating seeds, the main experimental results, and some new methods we are using to analyze the data to open the door for interpretative models of this phenomenon clarifying its function in the regulation and communication between cells and living organisms. We also discuss ideas on how to increase the signal-to-noise ratio of the measured signal to open up new experimental possibilities that allow the measurement and the characterization of currently unmeasurable quantities.

We study the emission of photons from germinating seeds using an experimental technique designed to detect light of extremely small intensity. We analyze the dark count signal without germinating seeds as well as the photon emission during the germination process. The technique of analysis adopted here, called diffusion entropy analysis (DEA) and originally designed to measure the temporal complexity of astrophysical, sociological and physiological processes, rests on Kolmogorov complexity. The updated version of DEA used in this paper is designed to determine if the signal complexity is generated either by non-ergodic crucial events with a non-stationary correlation function or by the infinite memory of a stationary but non-integrable correlation function or by a mixture of both processes. We find that dark count yields the ordinary scaling, thereby showing that no complexity of either kinds may occur without any seeds in the chamber. In the presence of seeds in the chamber anomalous scaling emerges, reminiscent of that found in neuro-physiological processes. However, this is a mixture of both processes and with the progress of germination the non-ergodic component tends to vanish and complexity becomes dominated by the stationary infinite memory. We illustrate some conjectures ranging from stress induced annihilation of crucial events to the emergence of quantum coherence.

High resolution (k = 18 Å⁻¹ or k = 17 Å⁻¹) copper K-edge EXAFS and MXAN (Minuit X-ray Absorption Near Edge) analyses have been used to investigate the structure of dissolved [Cu(aq)]²⁺ in 1,3-propanediol (1,3-P) or 1,5-pentanediol (1,5-P) aqueous frozen glasses. EXAFS analysis invariably found a single axially asymmetric 6-coordinate (CN6) site, with 4×O_eq = 1.97 Å, O_ax1 = 2.22 Å, and O_ax2 = 2.34 Å, plus a second-shell of 4×O_water = 3.6 Å. However, MXAN analysis revealed that [Cu(aq)]²⁺ occupies both square pyramidal (CN5) and axially asymmetric CN6 structures. The square pyramid included 4×H₂O = 1.95 Å and 1×H₂O = 2.23 Å. The CN6 sites included either a capped, near perfect, square pyramid with 5×H₂O = 1.94 ± 0.04 Å and H₂O_ax = 2.22 Å (in 1,3-P) or a split axial configuration with 4×H₂O = 1.94, H₂O_ax1 = 2.14 Å, and H₂O_ax2 = 2.28 Å (in 1,5-P). The CN6 sites also included an 8-H₂O second-shell near 3.7 Å, which was undetectable about the strictly pyramidal sites. Equatorial angles averaging 94° ± 5° indicated significant departures from tetragonal planarity. MXAN assessment of the solution structure of [Cu(aq)]²⁺ in 1,5-P prior to freezing revealed the same structures as previously found in aqueous 1M HClO₄, which have become axially compressed in the frozen glasses. [Cu(aq)]²⁺ in liquid and frozen solutions is dominated by a 5-coordinate square pyramid, but with split axial CN6 appearing in the frozen glasses. Among these phases, the Cu–O axial distances vary across 1 Å, and the equatorial angles depart significantly from the square plane. Although all these structures remove the ${\text{d}}_{{\text{x}}^2-{\text{y}}^2}$ , ${\text{d}}_{{\text{z}}^2}$ degeneracy, no structure can be described as a Jahn-Teller (JT) axially elongated octahedron. The JT-octahedral description for dissolved [Cu(aq)]²⁺ should thus be abandoned in favor of square pyramidal [Cu(H₂O)₅]²⁺. The revised ligand environments have bearing on questions of the Cu(i)/Cu(ii) self-exchange rate and on the mechanism for ligand exchange with bulk water. The plasticity of dissolved Cu(ii) complex ions falsifies the foundational assumption of the rack-induced bonding theory of blue copper proteins and obviates any need for a thermodynamically implausible protein constraint.