Lowest Energy Form Research Articles

Asymptotics of spectral functions of lower energy forms on weakly 1-complete manifolds

Let M be a weakly 1-complete manifold. We show that the optimal fundamental estimate holds true on M with mild conditions, then we establish the weak Morse inequalities for lower energy forms on M. We also study the case for q-convex manifolds.

Exploring the Use of "Honorary Transition Metals" To Push the Boundaries of Planar Hypercoordinate Alkaline-Earth Metals.

The quest for planar hypercoordinate atoms (phA) beyond six has predominantly focused on transition metals, with dodecacoordination being the highest reported thus far. Extending this bonding scenario to main-group elements, which typically lack d orbitals despite their larger atomic radius, has posed significant challenges. Intrigued by the potentiality of covalent bonding formation using the d orbitals of the heavier alkaline-earth metals (Ae = Ca, Sr, Ba), the so-called "honorary transition metals", we aim to push the boundaries of planar hypercoordination. By including rings formed by 12-15 atoms of boron-carbon and Ae centers, we propose a design scheme of 180 candidates with a phA. Further systematic screening, structural examination, and stability assessments identified 10 potential clusters with a planar hypercoordinate alkaline-earth metal (phAe) as the lowest-energy form. These unconventional structures embody planar dodeca-, trideca-, tetradeca-, and pentadecacoordinate atoms. Chemical bonding analyses reveal the important role of Ae d orbitals in facilitating covalent interactions between the central Ae atom and the surrounding boron-carbon rings, thereby establishing a new record for coordination numbers in the two-dimensional realm.

An Efficient Growth Pattern Algorithm (GrowPAL) for Cluster Structure Prediction.

Identifying the lowest energy isomers in large clusters is a major challenge. Here, we introduce the Growth Pattern Algorithm (GrowPAL), a new approach that generates initial seeds composed of n+1 atoms from the system with n atoms through an interstitial-type addition (I-type) mechanism. We evaluated the effectiveness of GrowPAL on Lennard-Jones (LJ) clusters with up to n = 80 atoms, verifying the algorithm's ability to find challenging minima such as LJ38 and the partially icosahedral LJ69 with fewer optimizations than existing methods. In addition, we discuss the advantages and limitations of GrowPAL using our deconstruction scheme, which identifies "forebears" structures to study growth pathways. Having evaluated the strengths and weaknesses of GrowPAL, we employed it to explore Sutton-Chen clusters containing 5 to 80 atoms, uncovering three new lowest energy forms. We then applied GrowPAL to boron clusters containing 8 to 15 atoms, successfully identifying all reported minima. Overall, GrowPAL offers a practical solution for efficiently identifying global minima in hierarchical systems, thereby reducing computational costs.

Amorphous Solid Forms of Ranolazine and Tryptophan and Their Relaxation to Metastable Polymorphs.

Different methods were explored for the amorphization of ranolazine, a sparingly soluble anti-anginal drug, such as mechanochemistry, quench-cooling, and solvent evaporation from solutions. Amorphous phases, with Tg values lower than room temperature, were obtained by cryo-milling and quench-cooling. New forms of ranolazine, named II and III, were identified from the relaxation of the ranolazine amorphous phase produced by cryo-milling, which takes place within several hours after grinding. At room temperature, these metastable polymorphs relax to the lower energy polymorph I, whose crystal structure was solved in this work for the first time. A binary co-amorphous mixture of ranolazine and tryptophan was produced, with three important advantages: higher glass transition temperature, increased kinetic stability preventing relaxation of the amorphous to crystalline phases for at least two months, and improved aqueous solubility. Concomitantly, the thermal behavior of amorphous tryptophan obtained by cryo-milling was studied by DSC. Depending on experimental conditions, it was possible to observe relaxation directly to the lower energy form or by an intermediate metastable crystalline phase and the serendipitous production of the neutral form of this amino acid in the pure solid phase.

Hierarchical Porous Metal-Organic Framework as Biocatalytic Microreactor for Enzymatic Biofuel Cell-Based Self-Powered Biosensing of MicroRNA Integrated with Cascade Signal Amplification.

Enzymatic biofuel cells have become powerful tools in biosensing, which however generally suffer from the limited loading efficiency as well as low catalytic activity and poor stability of bioenzymes. Herein, the hierarchical porous metal-organic frameworks (MOFs) are synthesized using tannic acid (TA) for structural etching, which realizes co-encapsulation of glucose dehydrogenase (GDH) and nicotinamide adenine dinucleotide (NAD+ ) cofactor in zeolitic imidazolate framework (ZIF-L) and are further used as the biocatalytic microreactors to modify bioanode. In this work, the TA-controlled etching can not only expand the pore size of microreactors, but also achieve the reorientation of enzymes in their lower surface energy form, therefore enhancing the biocatalysis of cofactor-dependent enzyme. Meanwhile, the topological DNA tetrahedron is assembled on the microreactors, which acts as the microRNA-responsive "lock" to perform the cascade signal amplification of exonuclease III-assisted target recycling on bioanode and hybridization chain reaction (HCR) on biocathode. The proposed self-powered biosensor has achieved a detection limit as low as 2 aM (6 copies miRNA-21 in a 5µL of sample), which is further successfully applied to identify cancer cells and clinical serums of breast cancer patients based on the different levels of miRNA-21, holding great potential in accurate disease identification and clinical diagnosis.

Pyridine Dimers and Their Low-Temperature Isomerization: A High-Resolution Matrix-Isolation Spectroscopy Study.

The bonding between two neutral aromatic compounds, especially small ones, has been controversially debated in the last decades, and terms like "π-stacking" had to be revised. Surprisingly, despite of many experimental and computational work, there is still no clear consensus about the structure of and the bonding in the pyridine dimer. In this work, for different isomeric forms of the pyridine dimer, the structures and bonding were elucidated by combining high-resolution matrix-isolation spectroscopic results with quantum-chemical calculations. High-resolution IR spectra of Ne matrices at 4 K containing pyridine were recorded for different concentrations and upon annealing to 10 and 12 K, relying on three isotopologues of pyridine. The spectra show the presence of hydrogen-bonded, T-shaped, and stacked forms of weakly-bound pyridine dimers. Among these, the hydrogen-bonded isomer is identified as the lowest-energy form. The results provide for the first time conclusive information about the interaction between two pyridine dimers.

Protomers of the green and cyan fluorescent protein chromophores investigated using action spectroscopy.

The photophysics of biochromophore ions often depends on the isomeric or protomeric distribution, yet this distribution, and the individual isomer contributions to an action spectrum, can be difficult to quantify. Here, we use two separate photodissociation action spectroscopy instruments to record electronic spectra for protonated forms of the green (pHBDI+) and cyan (Cyan+) fluorescent protein chromophores. One instrument allows for cryogenic (T = 40 ± 10 K) cooling of the ions, while the other offers the ability to perform protomer-selective photodissociation spectroscopy. We show that both chromophores are generated as two protomers when using electrospray ionisation, and that the protomers have partially overlapping absorption profiles associated with the S1 ← S0 transition. The action spectra for both species span the 340-460 nm range, although the spectral onset for the pHBDI+ protomer with the proton residing on the carbonyl oxygen is red-shifted by ≈40 nm relative to the lower-energy imine protomer. Similarly, the imine and carbonyl protomers are the lowest energy forms of Cyan+, with the main band for the carbonyl protomer red-shifted by ≈60 nm relative to the lower-energy imine protomer. The present strategy for investigating protomers can be applied to a wide range of other biochromophore ions.

Copper based nano Materials-Enhanced phase change materials with great potential for improved thermal energy storage properties

Thermal energy storage using nano materials as PCMs is a promising technology for generating low cost dispatchable electrical energy form solar power system. In this paper, synthesis of Cu based nano PCMs for thermal storage applications have been investigated. The nano copper particles are dispersed into the base fluid (PEG) in different weight percentage (0.5, 1 and 3 wt%) and addition of Cu nano particles effects on the thermo-physical properties have been investigated. The nano copper based phase change materials were characterized by X-ray diffraction, FTIR, TGA, DSC and thermal conductivity. Thermal conductivity increases with increasing Cu nano particles contents. Based on the results, nano phase change materials (3 wt%) samples shows the best performance of thermal energy storage properties amongst the other nano PCMs.

Conformation and equilibrium molecular structure of isoniazid in the gas phase

Equilibrium structure of anti-tuberculosis drug isoniazid has been determined for the first time by joint application of gas electron diffraction (GED) and quantum-chemical (QC) calculations. Employment of QC calculations revealed the possibility of free isoniazid molecules to exist as a mixture of four conformers with different configuration of the hydrazide group. However, only one conformer was taken into account for fitting GED data, as the others were estimated to be present in insufficient quantities in vaporous phase by QC computations. The reasons of stability of the lowest energy form have been discussed in a view of NBO analysis. The GED values have been compared with those obtained from QC computations and X-ray diffraction studies.

Cáncer en animales, el ambiente influye?

When talking about cancer, we know that there is an increase in cases in animals, including humans. Due to the close contact with people, there is a greater emphasis on the study and treatment of cancer in companion animals, since by living under similar conditions and developing the same types of cancer they can function as sentinels and models for their study. Cancer development revolves around alterations of genetic material, environmental influence, and interactions of the immune system. Here is a review of some carcinogenic factors inherent to the individual, such as race, gender and age, and external factors such as pollutants in the environment, in the air, water and land, and even in food. Ionizing radiation affects DNA and causes cancer, and there are other lower-energy forms of radiation that must be studied to prove or rule out their long-term carcinogenic effect.

H4HBEDpa: Octadentate Chelate after A. E. Martell.

H4HBEDpa, a new octadentate chelator inspired by the 1960s ligand HBED of Arthur E. Martell, has been investigated for a selection of trivalent metal ions useful in diagnostic and therapeutic applications (Sc3+, Fe3+, Ga3+, In3+, and Lu3+). Complex formation equilibria were thoroughly investigated using combined potentiometric and UV-vis spectrophotometric titrations which revealed effective chelation and high metal-sequestering capacity, in particular for Fe3+, log KFeL = 36.62, [Fe(HBEDpa)]-. X-ray diffraction study of single crystals revealed that the ligand is preorganized and forms hexa-coordinated complexes with Fe3+ and Ga3+ at acidic pH. Density functional theory (DFT) calculations were applied to probe the geometries and energies of all the possible conformers of [M(HBEDpa)]- (M = Sc3+, Fe3+, Ga3+, In3+, and Lu3+). DFT calculations confirmed the experimental findings, indicating that [Fe(HBEDpa)]- is bound tightly in an asymmetric pattern as compared to the symmetrically bound and more open [Ga(HBEDpa)]-, prone to hydrolysis at higher pH. DFT calculations also showed that a large metal ion such as Lu3+ fully coordinates with HBEDpa4-, forming a binary octadentate complex in its lowest-energy form. Smaller metal ions form six or seven coordinate complexes with HBEDpa4-.

6,6′-Dimethyl-1,1′,5,5′-tetraaza-6,6′-bi(bicyclo[3.1.0]hexane): synthesis and investigation of molecular structure by quantum-chemical calculations, NMR spectroscopy and X-ray diffraction analysis

A new diaziridine derivative with two bicyclic diaziridine-containing moieties in one molecule, 6,6′-dimethyl-1,1′,5,5′-tetraaza-6,6′-bi(bicyclo[3.1.0]hexane) (BiDiMDAH), has been synthesized for the first time. Its molecular structure has been investigated in the gas phase by means of quantum-chemical (QC) calculations, in CDCl3 solution by 1D and 2D NMR spectroscopy and in the solid state by the X-ray diffraction (XRD) technique. It was found by QC calculations that BiDiMDAH molecule in a free state presents a single conformer of C2 symmetry with trans orientation of the methyl groups about two carbons connecting diaziridine cycles. The 5-memebered rings in BiDiMDAH molecule has been found to be essentially planar. In order to explain conformational preferences of BiDiMDAH, natural bond orbitals (NBO) and atoms in molecules (AIM) analyses have been performed. According to the XRD data, BiDiMDAH crystallizes in space group P21/c with molecular structure resembling the structure obtained by the means of QC calculations for the lowest energy form. However, the relative arrangement of the methyl groups of the solid BiDiMDAH molecule is similar to that of the one of the transition states. The data of NMR spectroscopy has revealed that only one conformer is present in CDCl3 solution in agreement with the data of QC and XRD studies. The gaseous standard enthalpy of formation of BiDiMDAH has been estimated to be 106.1±1.2 kcal/mol by means of G4 theory.

Spatial Structure of the Acth-(6-9)-PGP Molecule

The spatial structure of ACTH-(6-9)-PGP molecule has been investigated using theoretical conformational analysis method. Amino acid sequence of the N-terminal pentapeptide fragment of His-Phe-Arg-Trp-Pro of this molecule conforms to the fragment 6-9 of ACTH hormone. Calculations of conformational states of this molecule are carried out regarding nonvalent, electrostatic and torsional interactions and the energy of hydrogen bonds. The spatial structure of the His-Phe-Arg-Trp-Pro-Gly-Pro molecule was estimated on the low–energy conformations of the N-terminal tetrapeptide fragment His-Phe-Arg-Trp and C-terminal tripeptide fragment Pro-Gly-Pro of this molecule. It is shown that the spatial structure of heptapeptide molecule can be presented by 11 low-energy forms of the main chain. The low–energy conformations of this molecule, the values of dihedral angles of the backbone and side chains of the amino acid residues were founded and the energies of intra- and inter-residual interactions were determined.

Spatial Structure of the Acth-(6-9)-PGP Molecule

The spatial structure of ACTH-(6-9)-PGP molecule has been investigated using theoretical conformational analysis method. Amino acid sequence of the N-terminal pentapeptide fragment of His-Phe-Arg-Trp-Pro of this molecule conforms to the fragment 6-9 of ACTH hormone. Calculations of conformational states of this molecule are carried out regarding nonvalent, electrostatic and torsional interactions and the energy of hydrogen bonds. The spatial structure of the His-Phe-Arg-Trp-Pro-Gly-Pro molecule was estimated on the low–energy conformations of the N-terminal tetrapeptide fragment His-Phe-Arg-Trp and C-terminal tripeptide fragment Pro-Gly-Pro of this molecule. It is shown that the spatial structure of heptapeptide molecule can be presented by 11 low-energy forms of the main chain. The low–energy conformations of this molecule, the values of dihedral angles of the backbone and side chains of the amino acid residues were founded and the energies of intra- and inter-residual interactions were determined.

Studying the hydrogen atom position in the strong-short intermolecular hydrogen bond of pure and 5-substituted 9-hydroxyphenalenones by invariom refinement and ONIOM cluster computations

Abstract The solid-state structures of three H-bonded enol forms of 5-substituted 9-hydroxyphenalenones were investigated to accurately determine the H atom positions of the intramolecular hydrogen bond. For this purpose, single-crystal X-ray diffraction (SC-XRD) data were evaluated by invariom-model refinement. In addition, QM/MM computations of central molecules in their crystal environment show that results of an earlier standard independent atom model refinement, which pointed to the presence of a resonance-assisted hydrogen bond in unsubstituted 9-hydroxyphenalone, are misleading: in all our three and the earlier solid-state structures the lowest energy form is that of an asymmetric hydrogen bond (CS form). Apparent differences of results from SC-XRD and other analytical methods are explained.

Two-dimensional low-energy scattering of a quantum particle in the summed field of Coulomb and power-law potentials

We study the two-dimensional scattering of a quantum particle by the force center acting on this particle via a superposition of a Coulomb potential and a power-law potential V0r−β with the exponent β ∈ (1,2). We find the explicit low-energy asymptotic forms of all partial phases and scattering amplitudes.

Exciplex formation as an approach to selective Copper(II) fluorescent sensors

The fluorescence of TB-cyclen (1,4,7,10-tetrabenzyl-1,4,7,10-tetraaza-cyclododecane) and its complexes with CuII, CdII, PbII, ZnII, HgII and AgI are reported in 50% (v/v) CH3OH/H2O. It appears, as supported by NMR studies, that the TB-cyclen undergoes slow protonation reactions in CH3CN with 0.01 M HClO4 present. The non-protonated TB-cyclen adopts the ++−− conformer that is sterically shielded from protonation and complex-formation, and the slow formation of the protonated forms of the ligand, and formation of the ++++ conformer, is required before complex-formation can occur. Strong emissions at 352 nm are oberved on formation of TB-cyclen complexes with CuII, CdII, PbII, but not with ZnII, HgII and AgI: it is suggested that these are exciplex emissions. The selectivity of the fluorescence of CuII with TB-cyclen compared to ZnII suggests that ligands of this type might be useful in sensing CuII in neural tissue, as in the case of studying Alzheimer’s disease, where potentially interefering metal ions such as CdII or PbII should not be present. The structure of [Pb(TB-cyclen)](ClO4)2 is reported, which shows that Pb···C π contacts are formed to all four N-benzyl groups. Structures of [Cd(TB-cyclen)CH3CN](ClO4)2 and [Hg(TB-cyclen)CH3CN](ClO4)2 are reported, that show M···C π contacts to only two of the N-benzyl groups, but the non-formation of four π contacts may be due to the presence of coordinated CH3CN molecules. The structure of [TB-cyclenH]ClO4 shows that the cyclen moeity of the ligand has the ++++ conformer required for complex-formation with metal ions. It is suggested that in the protonated forms of the free ligand, the ++++ conformer is stabilized with the N-benzyl groups in an upright position by the formation of NH···C π contacts, and CH···C π contacts between the upright N-benzyl groups. DFT calculations are carried out that show the structure of the exciplex that can be formed in the free (non-protonated) form of DB-cyclen, and show that its ++−− conformer is the lowest energy form.

Ultra-dense hydrogen H(0) as dark matter in the universe: new possibilities for the cosmological red-shift and the cosmic microwave background radiation

50 experimental publications exist on ultra-dense hydrogen H(0) from our laboratory. A review of these results was published recently (L. Holmlid and S. Zeiner-Gundersen in Phys. Scr. 74(7), 2019, https://doi.org/10.1088/1402-4896/ab1276). The importance of this quantum material in space is accentuated by a few recent publications: The so called extended red emission (ERE) spectra in space agree well (L. Holmlid in Astrophys. J. 866:107, 2018a) with rotational spectra measured from H(0) in the laboratory, supporting the notion that H(0) is a major part of the dark matter in the Universe. The proton solar wind was shown to agree well with the protons ejected by Coulomb explosions in p(0), thus finally providing a convincing detailed energy mechanism for the solar wind protons (L. Holmlid in J. Geophys. Res. 122:7956–7962, 2017c). The very high corona temperature in the Sun is also directly explained (L. Holmlid in J. Geophys. Res. 122:7956–7962, 2017c) as caused by well-studied nuclear reactions in H(0). H(0) is the lowest energy form of hydrogen and H(0) is thus expected to exist everywhere where hydrogen exists in the Universe. The so called cosmological red-shifts have earlier been shown to agree quantitatively with stimulated Raman processes in ordinary Rydberg matter. H(0) easily transforms to ordinary Rydberg matter and can also form the largest length scale of matter, with highly excited electrons just a few K from the ionization limit. Such electronic states provide the small excitations needed in the condensed matter H(0) for a thermal emission at a few K temperature corresponding to the CMB, the so called cosmic microwave background radiation. These excitations can be observed directly by ordinary Raman spectroscopy (L. Holmlid in J. Raman Spectrosc. 39:1364–1374, 2008b). A purely thermal distribution from H(0) and also from ordinary Rydberg Matter at 2.7 K is the simplest explanation of the CMB. The coupling of electronic and vibrational degrees of freedom observed as in experiments with H(0) gives almost continuous energy excitations which can create a smooth thermal CMB emission spectrum as observed. Thus, both cosmological red-shifts and CMB are now proposed to partially be due to easily studied microscopic processes in ultradense hydrogen H(0) and the other related types of hydrogen matter at the two other length scales. These processes can be repeated at will in any laboratory. These microscopic formation processes are much simpler than the earlier proposed large-scale non-repeatable processes related to Big Bang.

High-Resolution ENDOR Spectroscopy Combined with Quantum Chemical Calculations Reveals the Structure of Nitrogenase Janus Intermediate E4(4H).

We have shown that the key state in N2 reduction to two NH3 molecules by the enzyme nitrogenase is E4(4H), the "Janus" intermediate, which has accumulated four [e-/H+] and is poised to undergo reductive elimination of H2 coupled to N2 binding and activation. Initial 1H and 95Mo ENDOR studies of freeze-trapped E4(4H) revealed that the catalytic multimetallic cluster (FeMo-co) binds two Fe-bridging hydrides, [Fe-H-Fe]. However, the analysis failed to provide a satisfactory picture of the relative spatial relationships of the two [Fe-H-Fe]. Our recent density functional theory (DFT) study yielded a lowest-energy form, denoted as E4(4H)(a), with two parallel Fe-H-Fe planes bridging pairs of "anchor" Fe on the Fe2,3,6,7 face of FeMo-co. However, the relative energies of structures E4(4H)(b), with one bridging and one terminal hydride, and E4(4H)(c), with one pair of anchor Fe supporting two bridging hydrides, were not beyond the uncertainties in the calculation. Moreover, a structure of V-dependent nitrogenase resulted in a proposed structure analogous to E4(4H)(c), and additional structures have been proposed in the DFT studies of others. To resolve the nature of hydride binding to the Janus intermediate, we performed exhaustive, high-resolution CW-stochastic 1H-ENDOR experiments using improved instrumentation, Mims 2H ENDOR, and a recently developed pulsed-ENDOR protocol ("PESTRE") to obtain absolute hyperfine interaction signs. These measurements are coupled to DFT structural models through an analytical point-dipole Hamiltonian for the hydride electron-nuclear dipolar coupling to its "anchoring" Fe ions, an approach that overcomes limitations inherent in both experimental interpretation and computational accuracy. The result is the freeze-trapped, lowest-energy Janus intermediate structure, E4(4H)(a).

Quantum Chemical Rovibrational Characterization of CH2ClH+, a Low-Energy Isomer of Ionized Chloromethane

The astrophysical detection of chloromethane indicates that a low-energy form of the cation, the methyl chloronium cation (CH2ClH+), may also be found in similar regions. Quantum chemical computati...