Extracellular diffusion coupled with degradation is considered a dominant mechanism behind the establishment of morphogen gradients. However, the fundamental nature of these biophysical processes, visa viz, the Bicoid (Bcd) morphogen gradient, remains unclear. Fluorescence correlation spectroscopy has recently revealed multiple modes of Bcd transport at different spatial and temporal locations across the embryo. Here, we show that these observations are best fitted by a model fundamentally based on quantum mechanics. It is thus hypothesized that the transient quantum coherences in collaboration with unitary noise are responsible for the observed dynamics and relaxation to a non-equilibrium steady-state of the Bcd morphogen gradient. Furthermore, simulating the associated probability distribution for the model shows that the observed non-zero concentration of the Bcd molecules in the posterior-most parts of the embryo is a result of non-Gaussian distribution characteristic to quantum evolution. We conclude that with the Bcd gradient being essentially a one-dimensional problem, a simple one-dimensional model suffices for its analysis.

Extracellular diffusion coupled with degradation is considered as the dominant mechanism behind the establishment of morphogen gradients. However, the fundamental nature of these biophysical processes visa viz the Bicoid (Bcd) morphogen gradient remains unclear. Fluorescence correlation spectroscopy (FCS) has recently revealed multiple modes of Bcd transport at different spatial and temporal locations across the embryo. We here show that these observations, and a few others, are fitted by a model fundamentally based on quantum mechanics. We also indicate that the abstract and auxiliary feature called chirality of the said formalism finds a natural expression in our model of the Bcd gradient formation that might be verified in future experiments on the system.

The establishment and interpretation of the concentration distribution of the morphogen Bicoid (BCD) is considered crucial for the successful embryonic development of fruit flies. However, the biophysical mechanisms behind the timely formation and subsequent interpretation of the BCD morphogen by its target genes are not yet completely understood. Here a discrete-time, one-dimensional quantum walk model of BCD gradient formation is used to explain both the observed values of diffusivity and its precise interpretation. It is shown that the decoding of positional information from the BCD morphogen by its primary target gene hb, with the observed precision of ∼ 10%, takes a time period of less than a second, as expected on the basis of recent experimental observations. From this the on-rate (kon) for the binding of BCD to its target loci is obtained. Furthermore, the model is also used to explain certain key observations of recent optogenetic experiments concerning the time windows for BCD interpretation. Finally, it is argued that the presented model represents a significant step in the utilization of quantum computation-based techniques in studying the dynamics of biological systems in general and in the field of developmental biophysics in particular.

An atom trapped in a crystal vacancy, a metal cage, or a fullerene might have many immediate neighbors. Then, the familiar concept of valency or even coordination number seems inadequate to describe the environment of that atom. This difficulty in terminology is illustrated here by four systems: H atoms in tetragonal-pyramidal rhodium cages, H atom in an octahedral cobalt cage, H atom in a MgO octahedral hole, and metal atoms in C20 fullerenes. Density functional theory defines structure and energetics for the systems. Interactions of the atom with its container are characterized by the quantum theory of atoms in molecules (QTAIM) and the theory of non-covalent interactions (NCI). We establish that H atoms in H2Rh13(CO)243− trianion cannot be considered pentavalent, H atom in HCo6(CO)151− anion cannot be considered hexavalent, and H atom in MgO cannot be considered hexavalent. Instead, one should consider the H atom to be set in an environmental field defined by its 5, 6, and 6 neighbors; with interactions described by QTAIM. This point is further illustrated by the electronic structures and QTAIM parameters of M@C20, M=Ca to Zn. The analysis describes the systematic deformation and restoration of the symmetric fullerene in that series.

The establishment of graded concentration distributions of certain signalling molecules, called morphogens, is crucial for the successful embryonic development of multicellular organisms. The morphogen system that has been studied in the greatest detail is the Bicoid (Bcd) gradient established during the early embryonic development of fruit flies and provides the embryo cells with the necessary positional information for the proper implementation of the body plan of the organism. Both continuous as well as discrete-state classical random-walk models fail to provide a completely satisfactory explanation of the dynamics of Bcd gradient formation within the developmentally relevant timescales. By presuming the existence of an arbitrary chirality degree of freedom that characterizes each Bcd molecule, we here therefore develop a discrete-time quantum walk model of the process. Our approach is based on the recent suggestion that high temperatures and random interactions need not necessarily destroy many-body quantum coherence. In this way we are led to a system of non-classical master equations bearing an interference term that can be numerically solved on a computer. Our analysis predicts a large value of diffusion rate for the Bcd system in the very early nuclear division cycles that needs to be verified experimentally. Additionally, with the chirality and position degrees of freedom at our disposal entanglement shows up as a natural consequence in the system. Taking inspiration from a very recent demonstration of the existence of entanglement phenomenon in a hot, strongly-interacting atomic system, the discussion takes the point of view that the emergence of geometry in the embryo system is consequence of quantum entanglement that needs further understanding and analysis.

Abstract Zinc and cadmium atoms from laser ablation of the metals and mercury atoms ablated from a dental amalgam target react with HCN in excess argon during deposition at 5 K to form the MCN and MNC molecules and CN radicals. UV irradiation decreases the higher energy ZnNC isomer in favor of the lower energy ZnCN product. Cadmium and mercury atoms produce analogous MCN primary molecules. Laser ablation of metals also produces plume radiation which initiates H‐atom detachment from HCN. The freed H atom can add to CN radical to produce the HNC isomer. The argon matrix also traps the higher energy but more intensely absorbing isocyanide molecules. Further reactions with H atoms generate HMCN and HMNC hydrides, which can be observed by virtue of their C−N stretches and intense M−H stretches. Computational modeling of IR spectra and relative energies guides the identification of reaction products by providing generally reliable frequency differences within the Zn, Cd and Hg family of products, and estimating isotopic shifts using to 13C and 15N isotopic substitution for comparison with experimental data.

The title compound is a small molecule with many structural variations; it can illustrate a variety of internal hydrogen bonds, among other noncovalent interactions. Here we examine structures displaying hydrogen bonding between carbonyl oxygen and hydroxyl H; between carbonyl oxygen and amino H; hydroxyl H and amino N; hydroxyl O and amino H. We also consider H-bonding in its tautomer 2-oxopropanamide. By extrapolation algorithms applied to Hartree-Fock and correlation energies as estimated in HF, MP2, and CCSD calculations using the cc-pVNZ correlation-consistent basis sets (N = 2, 3, and 4) we obtain reliable relative energies of the isomeric forms. Assuming that such energy differences may be attributed to the presence of the various types of hydrogen bonding, we attempt to infer relative strengths of types of H-bonding. The Atoms in Molecules theory of Bader and the Local Vibrational Modes analysis of Cremer and Kraka are applied to this task. Hydrogen bonds are ranked by relative strength as measured by local stretching force constants, with the stronger =O…HO- > NH…O= > -OH…N well separated from a cluster > NH…O= ≈ >NH…OH ≈ CH…O= of comparable and intermediate strength. Weaker but still significant interactions are of type CH…N which is stronger than CH…OH.

While first-row transition metal cations, notably Fe(+), catalyze the gas-phase conversion of acetylene to benzene, a distinct path is chosen in systems with Os, Ir, and Rh cations. Rather than losing the metal cation M(+) from the benzene–M(+) complex, as is observed for the Fe(+) system, the heavy metal ions activate CH bonds. The landmark system C4H4-Os(+) reacts with acetylene to produce C6H4-Os(+) and dihydrogen. Following our work on isomers of the form C2nH2n-Fe(+), we show by DFT modeling that the CH bonds of the metalla-7-cycle structure, C6H6-Os(+), are activated and define the gas-phase reaction path by which H2 is produced. The landmark structures on the network of reaction paths can be used as a basis for the discussion of reactions in which a single Os atom on an inert surface can assist reactions of hydrocarbons.

The possibility of carbon tetravalence in geometries other than tetrahedral and of carbon hypervalence has been taken seriously since the 1970s. Computational modeling and subsequent experimental validation have established the existence of molecules with carbon atoms with planar tetravalence and as many as six objects in carbon’s coordination sphere. In this work, we develop insight into the nature of bonding to carbon in these unusual environs as provided by Bader’s Atoms in Molecules (AIM) analysis of the electron density, along with the electron localization function (ELF) and the non-covalent index (NCI). We review several well-established systems (spiropentadiene dication, hexamethyl benzene dication, dimethanospiro[2.2]octaplane dication, and 1,8-dimethoxy-9-dimethoxyanthracene cation) and propose new D2d–symmetric variants of a hexacoordinated species.

Time-resolved transient absorption spectroscopy and computational analysis of D-π-A complexes comprising FeII donors and TiIV acceptors with the general formula RCp2Ti(C2Fc)2 (where RCp = Cp*, Cp, and MeOOCCp) and TMSCp2Ti(C2Fc)(C2R) (where R = Ph or CF3) are reported. The transient absorption spectra are consistent with an FeIII/TiIII metal-to-metal charge-transfer (MMCT) excited state for all complexes. Thus, excited-state decay is assigned to back-electron transfer (BET), the lifetime of which ranges from 18.8 to 41 ps. Though spectroscopic analysis suggests BET should fall into the Marcus inverted regime, the observed kinetics are not consistent with this assertion. TDDFT calculations reveal that the singlet metal-to-metal charge-transfer (1MMCT) excited state for the FeII/TiIV complexes is not purely MMCT in nature but is contaminated with the higher-energy 1Fc (d-d) state. For the diferrocenyl complexes, RCp2Ti(C2Fc)2, the ratio of MMCT to Fc centered character ranges from 57:43 for the Cp* complex to 85:15 for the MeOOCCp complex. For the diferrocenyl and monoferrocenyl complexes investigated herein, the excited-state lifetimes decrease with increased 1Fc character. The effect of CuI coordination was also analyzed by time-resolved transient absorption spectroscopy and reveals the elongation of the excited-state lifetime by 3 orders of magnitude to 63 ns. The transient spectra and TDDFT analysis suggest that the long-lived excited state in Cp2Ti(C2Fc)2·CuX (where X is Cl or Br) is a triplet iron species with an electron arrangement of TiIV-3FeII-CuI.

The production of complex molecules in ammonia-carbon dioxide ices is presumed to pass through species of formula H3N:CO2 with further addition of ammonia and carbon dioxide. One possible landmark, carbamic acid, H2NCOOH, has been implicated among the products of warming and irradiation of such ices. Experimental study of the IR spectra of residues has suggested the presence of related species, including weakly bound 1:1 and 2:1 complexes of ammonia with carbon dioxide, zwitterionic carbamic acid, ammonium carbamate, and the dimer of carbamic acid. We computed the energetics and vibrational spectra of these species as well as the complex between ammonia and carbamic acid for gas and condensed phases. By means of a new spectrum-matching scoring between computed and observed vibrational spectra, we infer species that are most probably present. The leading candidates are ammonium carbamate, the carbamic acid-ammonia complex, and the carbamic acid dimer.

The simplest ideas of antiaromaticity refer to regular monocyclic systems and the eigenfunctions of the Huckel Hamiltonian for 4n pi electrons in such systems. The antiaromaticity is expressed in the energy penalty for such idealized systems relative to the Huckel energy for 2n noninteracting pi pairs. Observed systems seldom achieve the regular planar geometry assumed in this picture, owing to their ability to ease the antiaromaticity penalty by departures from the regular geometry and also by export of the 4n pi electrons' charge to substituents. In this report we estimate numerical values for the stabilization derived from such departures from the structure and the charge distribution of the idealized antiaromatic cyclopropenyl anion for a specific case, 3-dehydro-3-methyl carboxylate cyclopropenyl anion 1(-) using the thermochemical scheme CBSQB3 supplemented by CCSD(T) calculations. According to the isodesmic reaction, the anion 1(-) is destabilized by about 10-15 kcal/mol relative to the saturated 3-dehydro-3-methylcarboxylate cyclopropyl anion 2(-). We propose that the anion relieves a portion of the antiaromatic destabilization by (a) pyramidalization of one carbon of the ring, and (b) export of negative charge into the ester substituent. Both of these responses are expressed in the equilibrium structure of the anion. In the course of the study we estimate the acidity of several related anions and the enthalpy of formation of their neutral conjugate acids, and describe the interconversion of 1 to the dehydrotriafulvalene anion 3(-) by reaction with CO2. [GRAPHICS] .

Purely organic phosphors have important applications in imaging, sensing, informatics and illumination. Methoxy-substituted difluoroboron dibenzoylmethane (BF2dbm) complexes exhibit intense fluorescence with an almost unity quantum yield. Here we show that by simply introducing an sp3 oxygen-bridged methoxylphenyl group as a pendant to BF2dbm, the boron complex exhibits a triplet quantum yield of 0.16, a more than 100-fold increase compared to that of BF2dbm.

Room-temperature phosphorescence (RTP)-based sensors have distinctive advantages over the fluorescence counterparts, such as larger Stokes shifts and longer lifetimes. Unfortunately, almost all RTP sensors are operated on quenching-based mechanisms given the sensitive nature of the emissive triplet state. Here we report a type of thioether RTP molecules that shows RTP "turn-on" when volatile acid vapors such as HCl are in contact. To elucidate the underlying mechanism, model thioethers containing different donor/acceptor combinations are investigated via fluorescence spectroscopy and theoretical calculations aided by molecular coordinates obtained from single-crystal X-ray diffraction. It is revealed that a charge-transfer character in the phosphorescence state is crucial. The "turn-on" design concept may significantly broaden the sensing application scope for organic RTP molecules.

The preparation and properties of the complex (R-Mo,R)-MoTp(NO)(DMAP)(eta(2)-alpha-pinene) are described (similar to 10 g scale; DMAP = 4-(dimethylarnino)pyridine; Tp = hydridotris(pyrazolyl)borate). This complex undergoes exchange of the pinene with a wide range of other pi ligands including acetone, ethyl acetate, N,N-dimethylformamide, acetonitrile, and naphthalene. Treatment of the alpha-pinene cornplex with iodine results in the complex (S)-MoTp(NO)(DMAP)(I), which is recovered in enantioenriched form (er = 99:1; yield >90%; scale 4.6 g). Reduction of this molybdenum(I) precursor results in enantioenriched molybdenum(0) complexes, including (R)-MoTp-(NO)(DMAP)(eta(2)-trifluorotoluene). Sequential treatment of this arene complex with acid, a masked enolate, and iodine regenerates MoTp-(NO)(DMAP)(I) along with an alkylated 1-(trifluoromethyl)cyclohexa-1,3-diene with an er value as high as 99:1. This process demonstrates the efficient transfer of asymmetry from a-pinene to the diene product. Accompanying studies with (1R)-myrtenal reveal a redox-catalyzed pinene/myrtenal ligand exchange occurring through Mo(I) intermediates.

New gas phase infrared spectroscopy is reported for an aromatic alpha hydroxy carboxylic acid homo dimer of 9-hydroxy-9-fluorene carboxylic acid (9HFCA)(2), and the hetero dimer of 9HFCA with glycolic acid. In terms of the 9-hydroxy stretching frequency, the 16 cm(-1) blue-shift in the homo dimer and the 17 cm(-1) blue-shift in the hetero dimer, relative to that in 9HFCA monomer, are attributed to collective effects with anti-cooperativity stronger than cooperativity. Furthermore, for the hetero dimer, the two alpha hydroxy groups' stretching frequencies are clearly resolved, and differ by 30cm(-1). This difference represents a modest, quantitative enhancement of the intramolecular H-bond by the fluorene moiety in 9HFCA monomer, as opposed to that in glycolic acid. Accurate vibrational frequencies of the alpha OH, 3568 cm(-1) in the bare glycolic acid, and 3584 cm(-1) in the glycolic acid homo dimer are determined for the first time by comparison to 9HFCA monomer, homo and hetero dimers. The quantitative studies by infrared spectroscopy reveal subtle interactions among intra-and intermolecular H-bonds in the alpha hydroxyl acid dimers, which are also uniquely extended to probe each monomer's subtle intramolecular interactions.

Difluoroboron β-diketonates (BF2 bdks) show both fluorescence (F) and room-temperature phosphorescence (RTP) when confined to a rigid matrix, such as poly(lactic acid). These materials have been utilized as optical oxygen sensors (e.g., in tumors, wounds, and cells). Spectral features include charge transfer (CT) from the major aromatic donor to the dioxaborine acceptor. A series of naphthyl-phenyl dyes (BF2 nbm) (1-6) were prepared to test heavy-atom placement effects. The BF2 nbm dye (1) was substituted with Br on naphthyl (2), phenyl (3), or both rings (4) to tailor the fluorescence/phosphorescence ratio and RTP lifetime-important features for designing O2 sensing dyes by means of the heavy atom effect. Computational studies identify the naphthyl ring as the major donor. Thus, Br substitution on the naphthyl ring produced greater effects on the optical properties, such as increased RTP intensity and decreased RTP lifetime compared to phenyl substitution. However, for electron-donating piperidyl-phenyl dyes (5), the phenyl aromatic is the major donor. As a result, Br substitution on the naphthyl ring (6) did not alter the optical properties significantly. Experimental data and computational modeling show the importance of Br position. The S1 and T1 states are described by two singly occupied MOs (SOMOs). When both of these SOMOs have substantial amplitude on the heavy atom, passage from S1 to T1 and emission from T1 to S0 are both favored. This shortens the excited-state lifetimes and enhances phosphorescence.

Gas phase conversion of acetylene to benzene, assisted by a single metal cation such as Fe(+), Ru(+) and Rh(+), offers an attractive prospect for application of computational modelling techniques to catalytic processes. Gas phase processes are not complicated by environmental effects and the participation of a single metal atom is a significant simplification. Still the process is complex, owing to the possibility of several low-energy spin states and the abundance of alternative structures. By density functional theory modelling using recently developed models with range and dispersion corrections, we locate and characterise a number of extreme points on the FeC6H6(+) surface, some of which have not been described previously. These include eta-1, eta-2 and eta-3 complexes of Fe(+) with the C4H4 ring. We identify new FeC6H6(+) structures as well, which may be landmarks for the Fe(+)-catalysed production of benzene from acetylene. The Fe(+) benzene complex is the most stable species on the FeC6H6 cation surface. With the abundant energy of complexation available in the isolated gas phase species, detachment of the Fe(+) and production of benzene can be efficient. We address the issue raised by other investigators whether multi-configurational self-consistent field methods are essential to the proper description of these systems. We find that the relative energy of intrinsically multi-determinant doublets is strongly affected, but judge that the density functional theory (DFT) description provides more accurate estimates of energetics and a more plausible reaction path.[GRAPHICS].

Hydrogen (H) bonds are of fundamental importance in a wide range of molecular sciences. While the study of two-center H-bonding AH is well advanced, much remains to be learned in a quantitative and definitive manner for complexes with multiple H-bonds. Exemplary cases are in the category of alpha hydroxy carboxylic acids, i.e., the complexes of glycolic acid with water and formic acid. In glycolic acid, an intramolecular H-bond forms between the carboxyl group and the alpha OH group. The alpha OH stretching frequency may be affected upon complexing with water or formic acid. Direct study of glycolic acid complexes is unfortunately very difficult. However, an aromatic analogue, 9-hydroxy-9-fluorene carboxylic acid (9HFCA), permits detailed and accurate gas phase spectroscopic studies. Since computational analysis establishes that H-bonding is very similar from glycolic acid complexes to 9HFCA complexes, direct studies on 9HFCA complexes by laser spectroscopy also deduce new and subtle information for glycolic acid complexes in terms of molecular structures, binding strength, and collective effects of multiple H-bonds associated with anti-cooperativity and cooperativity.