Lowest Energy Form Research Articles

The geometry, vibrational frequencies, thermochemistry, quadrupole moments and electronic structure of C 2Na 2: Comparison with C 2Li 2, C 2H 2, C 2F 2 and C 2Cl 2

The electronic structure of Na 2C 2 is studied using ab initio electronic structure methods and is compared to the companion molecule Li 2C 2. Both the linear D ∞ h and planar structures are minima on the ground state potential surface with the planar D 2 h conformation being the lowest energy form, similar to Li 2C 2. At the CCSD(t) level the planar form is more stable that the linear by 11.2 kcal/mol as compared with 7.34 kcal/mol for Li 2C 2. Both molecules are significantly ionic. The vibrational frequencies, atomization energy at 0 K, D 0, and the standard enthalpy of formation, Δ H 0 f are calculated and compared to those of Li 2C 2 as well as HCCH, FCCF and ClCCCl. We find D 0 and Λ H 0 f to be 331.1 and 84.92 kcal/mol for Li 2C 2 and 298.3 and 93.25 kcal/mol for Na 2C 2. We calibrate these by calculating the same quantities for HCCH, FCCF and ClCCCl.

DFT Studies of the Molecular Structures and Conformational Processes of 1,2‐, 1,3‐ and 1,4‐Dithiepane

AbstractIn this study density functional theory (DFT) calculations at B3LYP/6‐31G(d), B3LYP/6‐31+G(d) and B3LYP/6‐311+G(2df,2p) levels for geometry optimization and total energy calculation were applied for investigation of the important energy‐minimum conformations and transition‐state of 1,2‐, 1,3‐, and 1,4‐dithiepanes. Moreover, ab initio calculations at HF/6‐31G(d) level of theory for geometry optimization and MP2/6‐311G(d)//HF/ 6‐31G(d) level for a single‐point total energy calculation were reported for different conformers. The obtained results reveal that, the twist‐chair conformer is a global minimum for all of these compounds. Also, two local minimum were found in each case, which are twisted‐chair and twisted‐boat conformers. The boat and chair geometries are transition states. The minimum energy conformation of 1,2‐dithiepane is more stable than the lowest energy forms of 1,3‐dithiepane and 1,4‐dithiepane. Furthermore, the anomeric effect was investigated for 1,3‐dithiepane by the natural bond orbital method. The computational results of this study shows that all conformers of 1,3‐dithiepane have a hypercojugation system. Finally, the 13C NMR chemical shifts for the conformers of 1,4‐dithiepane were calculated, which have good correlation with their experimental values.

A Delineation of Diketopiperazine Self-Assembly Processes: Understanding the Molecular Events Involved in Nϵ-(Fumaroyl)diketopiperazine of l-Lys (FDKP) Interactions

The Nepsilon-fumaroylated diketopiperazine of L-Lys (FDKP, 1) self-assembles into microparticles that can be used for pulmonary drug delivery. When these particles are formulated with insulin, the resultant powder (Technosphere Insulin) provides a novel prandial insulin therapy. To better understand the self-assembly of 1, a series of model compounds were synthesized that allowed for the determination of the preferred intramolecular hydrogen-bonding pattern of FDKP. Variable-temperature NMR (CDCl3) and FTIR studies of acyclic diamides (3-7a) and diketopiperazine models (7b- 9d) revealed the preference of a 10-membered hydrogen bond between one of the diketopiperazine's amido NH and the appended fumaramido-carbonyl (assigned as a "type B" H bond). Molecular modeling studies identified a low energy conformer in the architecture of 1, which contains two Nepsilon-fumaroylated lysine side chains appended to the diketopiperazine core. The lowest energy form involved a "cooperative" hydrogen bond motif which involved only one of the diketopiperazine amides and had one "arm" involved in a type B motif and the other in a "type A" hydrogen bond (i.e., the fumaramidyl NH H-bonding to the diketopiperazine amide carbonyl). This cooperative hydrogen bond scenario orients the appended fumaryl groups into a distinctive 90 degrees arrangement and is likely involved in its self-assembly into microparticles.

Constraining the low-energy pion electromagnetic form factor with spacelike data

The pionic contribution to the g−2 of the muon involves a certain integral over the modulus squared of $F_\pi(t)$, the electromagnetic form factor of the pion. We extend techniques that use cut-plane analyticity properties of $F_\pi(t)$ in order to account for present day estimates of the pionic contribution and experimental information at a finite number of points in the spacelike region. Using data from several experiments over a large kinematic range for $|t|$, we find bounds on the expansion coefficients of $F_\pi(t)$, sub-leading to the charge radius. The value of one of these coefficients in chiral perturbation theory respects these bounds. Furthermore, we present a sensitivity analysis to the inputs. A brief comparison with results in the literature that use observables other than the g−2 and timelike data is presented.

Revealing the multiple structures of serine.

We explored the conformational landscape of the proteinogenic amino acid serine [CH(2)OH CH(NH(2)) COOH] in the gas phase. Solid serine was vaporized by laser ablation, expanded in a supersonic jet, and characterized by Fourier transform microwave spectroscopy. In the isolation conditions of the jet there have been discovered up to seven different neutral (non-zwitterionic) structures of serine, which are conclusively identified by the comparison between the experimental values of the rotational and quadrupole coupling constants with those predicted by ab initio calculations. These seven forms can serve as a basis to represent the shape of serine in the gas phase. From the postexpansion abundances we derived the conformational stability trend, which is controlled by the subtle network of intramolecular hydrogen bonds formed between the polar groups in the amino acid backbone and the hydroxy side chain. It is proposed that conformational cooling perturbs the equilibrium conformational distribution; thus, some of the lower-energy forms are "missing" in the supersonic expansion.

Differential hedonic, sensory and behavioral changes associated with flavor–nutrient and flavor–flavor learning

Flavor–flavor and flavor–nutrient associations can modify liking for a flavor CS, while flavor–flavor associations can also modify the sensory experience of the trained flavor. Less is known about how these associations modify behavioral responses to the trained CS. To test this, 60 participants classified as sweet likers were divided into five training conditions with a novel flavor CS. In the flavor–flavor only condition, participants consumed the target CS in a sweetened, low-energy form, with energy (maltodextrin) but no sweetness added in the flavor–nutrient only condition and both energy and sweetness (sucrose) in the combined flavor–flavor, flavor–nutrient condition. Comparison groups controlled for exposure to the CS, and repeat testing. Training was conducted in a hungry state on four non-consecutive days. To test for acquired changes in evaluation and intake, the flavor CS was processed into a low-energy sorbet, which was evaluated and consumed ad libitum on test days before and after training. Liking for the flavor CS increased only in the sucrose-sweetened condition, but intake increased significantly in both high-energy conditions. In contrast, rated sweetness of the sorbet increased in both sucrose-sweetened and aspartame-sweetened conditions. These findings suggest that liking changes were maximal when flavor–flavor and flavor–nutrient associations co-occurred, but that behavioral changes were specific to flavor–nutrient associations.

Explicit mapping between a two-dimensional quantum Hall system and a one-dimensional Luttinger liquid. II. Correlation functions

We study a model of a quantum Hall system with the electrons confined to a narrow, linear channel. The system is mapped to a one-dimensional (1D) system which in the low-energy approximation has the form of a Luttinger liquid with different interactions between particles of equal and of opposite chiralities. In a previous paper (Part I) [M. Horsdal and J. M. Leinaas, Phys. Rev. B 76, 195321 (2007)], we studied this mapping at the microscopic level, and examined how the interaction in the two-dimensional (2D) system renormalizes 1D Luttinger liquid parameters. We follow up this study here and derive the low-energy form of the 2D electron correlation function by applying the mapping from the 1D correlation function. The derived expression has a natural separation in a bulk part, which is not modified by interactions, and an edge part, which is modified. We study the effect of interactions on the electron density and on the asymptotic form of the correlation function. The asymptotic parameter is found to be consistent with the expected value from the Luttinger liquid theory, but deviations from the asymptotic form are found in a rather wide intermediate interval. We suggest some questions of interest for further study.

The Low-Energy Forms of Photosystem I Light-Harvesting Complexes: Spectroscopic Properties and Pigment-Pigment Interaction Characteristics

In this work the spectroscopic properties of the special low-energy absorption bands of the outer antenna complexes of higher plant Photosystem I have been investigated by means of low-temperature absorption, fluorescence, and fluorescence line-narrowing experiments. It was found that the red-most absorption bands of Lhca3, Lhca4, and Lhca1–4 peak, respectively, at 704, 708, and 709 nm and are responsible for 725-, 733-, and 732-nm fluorescence emission bands. These bands are more red shifted compared to “normal” chlorophyll a (Chl a) bands present in light-harvesting complexes. The low-energy forms are characterized by a very large bandwidth (400–450 cm −1), which is the result of both large homogeneous and inhomogeneous broadening. The observed optical reorganization energy is untypical for Chl a and resembles more that of BChl a antenna systems. The large broadening and the changes in optical reorganization energy are explained by a mixing of an Lhca excitonic state with a charge transfer state. Such a charge transfer state can be stabilized by the polar residues around Chl 1025. It is shown that the optical reorganization energy is changing through the inhomogeneous distribution of the red-most absorption band, with the pigments contributing to the red part of the distribution showing higher values. A second red emission form in Lhca4 was detected at 705 nm and originates from a broad absorption band peaking at 690 nm. This fluorescence emission is present also in the Lhca4-N-47H mutant, which lacks the 733-nm emission band.

Methylsalicylate: A Rotational Spectroscopy Study

We report the free-jet rotational spectra of methylsalicylate, a molecule with a possible tautomeric and conformational equilibrium. In the ground electronic state, the molecule adopts a form stabilized by an intramolecular hydrogen bond between the phenolic hydrogen and the carbonylic oxygen, and this structure is characterized as the lowest-energy form by quantum chemical calculations. All rotational transitions are split because of the internal rotation of the methyl group, and the value of the barrier for this motion was determined to be V(3) = 5.38 kJ mol(-1).

Differential hedonic, sensory and behavioural changes associated with flavour–nutrient and flavour–flavour learning.

Flavour–flavour and flavour–nutrient associations can modify liking for a flavour CS, while flavour-flavour associations can also modify the sensory experience of the trained flavour. Less is known about how these associations modify behavioural responses to the trained CS. To test this, 72 participants classified as sweet likers according to their response to 10% sucrose were divided into five training conditions with a cranberry+orange flavour CS. In the flavour–flavour condition, participants consumed the target CS in a sweetened, low energy form (7 kcal, aspartame as sweetener), with energy but no sweetness added in the flavour-nutrient condition (159 kcal, energy as maltodextrin) and both energy and sweetness in a combined flavour–flavour, flavour–nutrient condition (159 kcal with 10% sucrose). Control groups controlled for exposure to the CS, and repeat testing. Training was conducted in a hungry state on four non-consecutive days. To test for acquired changes in evaluation and intake, the flavour CS was processed into a low-energy sorbet, which was evaluated and consumed ad libitum on two test days before and after training. Liking for the flavour CS increased only in the sucrose sweetened condition, but intake increased significantly in both high-energy conditions. In contrast, rated sweetness of the sorbet increased in both the sucrose–sweetened and aspartame–sweetened conditions. These findings suggest that liking changes are maximal when flavour–flavour and flavour–nutrient associations co-occur, but that behavioural changes are specific to flavour-nutrient associations. These data also confirm that hedonic and sensory evaluations occur through independent learning processes.

Raman spectra, ab initio calculations, phase transitions and conformations of 1,3-disilabutane

Raman spectra of 1,3-disilabutane (SiH3CH2SiH2CH3) were recorded as a liquid at room temperature and at 14 temperatures between 293 and 137 K. Spectra of an amorphous and annealed solid were recorded at 78 K, and very distinct changes occurred on crystallization. In the variable temperature Raman spectra, some bands changed in intensity and were interpreted in terms of conformational equilibria between the two possible conformers. Complete assignments were made for all the bands of the most stable conformer, anti. From three band pairs assigned to the anti and gauche conformers, the conformational enthalpy differences ΔH(gauche-anti) were found to be between 1.3 kJ mol−1 and 1.7 kJ mol−1, using peak heights, and the more stable anti conformer was present in the crystal. A lower value of 0 ± 0.3 kJ mol−1 was obtained employing band areas. Ab initio calculations in the RHF and MP2 approximations and DFT calculations were carried out pointing to the anti conformer as the low energy form.

Single Molecule Spectroscopy of Poly 3-octyl-thiophene (P3OT)

We report on the spectroscopy of isolated chains of P3OT, in a highly dilute solution in the inert polymer host poly(methyl-methacrylate) (PMMA). This environment permits a detailed analysis of emission transitions in the 1.9-2.2 eV range by suppressing the formation of the lowest emitting-energy aggregated form of P3OT. Herein it is observed that the 1.9-2.2 eV band is in fact split into low (red) and high (blue) energy forms in a highly analogous situation to that found for the conjugated polymer MEH-PPV. Another focus of this work is an investigation of the interaction of singlet and triplet excitons in P3OT. The results indicate that, like in MEH-PPV, triplet excitons are highly efficient fluorescence quenchers for P3OT, strongly quenching the fluorescence of P3OT under even relatively low excitation intensities.

Chiral recognition in a single molecule: a study of homo and heterochiral butan-2,3-diol by Fourier transform microwave spectroscopy

The microwave Fourier transform spectrum of butan-2,3-ol has been recorded in the range 5–18 GHz. The molecule possesses two chiral centres and exists in two distinct forms, one of which is homochiral ((R,R) or (S,S)) and is overall chiral, and the other which is heterochiral ((R,S) or (S,R)) and is overall meso. Detailed ab initio calculations enabled investigation of the relative stability of the many conformations exhibited by each form of the molecule. It is shown that the lowest energy forms in each case possess an internal hydrogen bond. The spectrum of the heterochiral (meso) form could be readily identified and analysed. The homochiral form, however, exhibits a tunnelling motion of about 1 GHz, in which the hydrogen bonded OH groups interchange their roles. Deuteration of one of these OH protons quenches the tunnelling motion, aiding the assignment of the spectrum. In all cases, deuteration of the hydroxyl groups was used to locate the positions of the OH hydrogen atoms and helped to confirm the identification of the conformers present.

Polymorphism of Scyllo-Inositol: Joining Crystal Structure Prediction with Experiment to Elucidate the Structures of Two Polymorphs

We report on the crystal structures of two polymorphs of scyllo-inositol. Crystallization of this inositol initially failed to yield a single crystal suitable for structure solution, so a computational prediction of the low-energy forms was performed in parallel with the crystallization experiments. When a single crystal was finally grown, its structure failed to explain the powder X-ray diffraction pattern of the bulk material, which seemed to show a mixture of polymorphs. With the aid of the lowest-energy predicted crystal structure from a lattice energy search and the DASH program for structure solution from powder data, we propose the structure of the second polymorph. The combined use of single-crystal structure solution, structure solution from powder diffraction data, and a lattice energy search for possible structures, which was necessary for the elucidation of the second polymorph of scyllo-inositol, demonstrates the synergy between experimental and computational studies of molecular organic materials.

Molecular Structures of Benzoic Acid and 2-Hydroxybenzoic Acid, Obtained by Gas-Phase Electron Diffraction and Theoretical Calculations

The structures of benzoic acid (C6H5COOH) and 2-hydroxybenzoic acid (C6H4OHCOOH) have been determined in the gas phase by electron diffraction using results from quantum chemical calculations to inform restraints used on the structural parameters. Theoretical methods (HF and MP2/6-311+G(d,p)) predict two conformers for benzoic acid, one which is 25.0 kJ mol(-1) (MP2) lower in energy than the other. In the low-energy form, the carboxyl group is coplanar with the phenyl ring and the O-H group eclipses the C=O bond. Theoretical calculations (HF and MP2/6-311+G(d,p)) carried out for 2-hydroxybenzoic acid gave evidence for seven stable conformers but one low-energy form (11.7 kJ mol(-1) lower in energy (MP2)) which again has the carboxyl group coplanar with the phenyl ring, the O-H of the carboxyl group eclipsing the C=O bond and the C=O of the carboxyl group oriented toward the O-H group of the phenyl ring. The effects of internal hydrogen bonding in 2-hydroxybenzoic acid can be clearly observed by comparison of pertinent structural parameters between the two compounds. These differences for 2-hydroxybenzoic acid include a shorter exocyclic C-C bond, a lengthening of the ring C-C bond between the substituents, and a shortening of the carboxylic single C-O bond.

Influence of the Photosystem I−Light Harvesting Complex I Antenna Domains on Fluorescence Decay

The time-resolved fluorescence decay of plant PSI-LHCI has been analyzed and compared with its component parts, the PSI core and the peripheral antenna LHCI, in an attempt to (i) define the physical domains associated with the multicomponent decay-associated spectra (DAS) and determine the origin of the kinetically slow steps responsible for them, (ii) formulate a clear working hypothesis for the positive decay-associated spectral amplitudes of the two slowest decay components, and (iii) determine the impact of the peripheral antenna complexes (LHCI) on the effective trapping rate for the photosystem. The results for PSI-LHCI indicate that the three exponential component DAS description, previously reported in the literature, is not numerically unique. The fit minimum is rather broad, which necessitated the introduction of other fit criteria in addition to the purely numerical one. The analysis demonstrates that (i) the physical domains associated with the multicomponent decay are associated with the antenna and particularly with the low-energy spectral forms, (ii) the positive DAS amplitudes of the two slowest decay components are suggested to be due to energy transfer kinetic heterogeneity to different F735 low-energy forms, and (iii) the peripheral antenna slows down the effective photosystem photochemical rate by about 3 times, and this is approximately half due to antenna degeneracy and half due to the low-energy forms.

Dynamics of flexible cycloalkanes. Ab initio and DFT study of the conformational energy hypersurface of cyclononane

The multidimensional Potential Energy Hypersurface (PEHS) for the cyclononane molecule was comprehensively investigated at the Hartree-Fock (HF), and Density Functional Theory (DFT) levels of theory. Second-order Møller-Plesset perturbation theory (MP2) optimizations were also carried out to confirm the low-energy conformations. The previously reported Geometrical Algorithm to Search Conformational Space (GASCOS) has been used to generate the starting geometries for the conformational analysis. The GASCOS algorithm combined with ab initio and DFT optimization permits searching of the potential energy hypersurface for all minimum-energy conformations as well as transition structures connecting the low-energy forms. The search located all previously reported structures together with 11 transition states, some of which were not found by earlier searching techniques. Altogether, 16 geometries (five low-energy conformations and 11 transition states) were found to be important for a description of the conformational features of cyclononane. RB3LYP/aug-cc-pVTZ//RB3LYP/6-31G(d) calculations suggest a conformational mixture between the twist boat-chair and twist chair-boat conformations as the preferred forms. In addition only the twist chair-chair conformation with 1.52 kcal/mol above the global minimum should contribute somewhat to the equilibrium mixture of conformations. Our results allow us to form a concise idea about the internal intricacies of the 9D vector space describing the conformation of cyclononane as well as the associated conformational potential energy hypersurface of nine independent variables.

Conformational stability and normal coordinate analyses of imidoylketene O [dbnd6]C [dbnd6]CH–CH [dbnd6]NH

The conformational and structural stability of imidoylketene O C CH–CH NH were investigated by DFT-B3LYP and ab initio MP2 calculations with the 6-311+G** basis set. From the calculations imidoylketene was predicted to exist predominantly in a mixture of trans– anti (the CCCN dihedral angle is 180°) and cis– anti (the CCCN dihedral angle is 0°) conformations with the trans– anti being the lower energy form. The two anti conformations were predicted to have a comparable relative stability with the C–C rotational barrier of about 9–10 kcal/mol at DFT-B3LYP and MP2 calculations. The equilibrium constanat for the trans⇔ cis conformational conversion of the two anti forms of imidoylketene was calculated to be 0.4432 kcal/mol that corresponds to an equilibrium mixture of about 31% cis– anti and 69% trans– anti at 300 K. The vibrational frequencies were computed at the DFT-B3LYP level and the infrared and Raman spectra of the molecule were calculated. Complete vibrational assignments were made on the basis of normal coordinate analyses.

A Microwave and Quantum Chemical Study of the Conformational Properties and Intramolecular Hydrogen Bonding of 1-Fluorocyclopropanecarboxylic Acid

The structural and conformational properties of 1-fluorocyclopropanecarboxylic acid have been explored by microwave spectroscopy and a series of ab initio (MP2/6-311++G(d,p) level), density functional theory (B3LYP/aug-cc-pVTZ level), and G3 quantum chemical calculations. Four "stable" conformers, denoted conformers I-IV, were found in the quantum chemical calculations, three of which (conformers I -III) were predicted to be low-energy forms. Conformer I was in all the quantum chemical calculations predicted to have the lowest energy, conformer III to have the second lowest energy, and conformer II to have the third lowest energy. Conformers II and III were calculated to have relatively large dipole moments, while conformer I was predicted to have a small dipole moment. The microwave spectrum was investigated in the 18-62 GHz spectral range. The microwave spectra of conformers II and III were assigned. Conformer I was not assigned presumably because its dipole moment is comparatively small. Conformer II is stabilized by an intramolecular hydrogen bond formed between the fluorine atom and the hydrogen atom of the carboxylic acid group. Conformer III has a synperiplanar orientation for the F-C-C=O and H-O-C=O chains of atoms. Its dipole moment is: mua = 3.4(10), mub = 10.1(13), and muc = 0.0 (assumed) and mu(tot) = 10.6(14) x 10(-30) C m [3.2(4) D]. Several vibrationally excited states of the lowest torsional mode of each of II and III were also assigned. The hydrogen-bonded conformer II was found to be 2.7(2) kJ/mol less stable than III by relative intensity measurements. Absolute intensity measurements were used to show that the unassigned conformer I is the most abundant form present at a concentration of roughly 65% at room temperature. Conformer I was estimated to be ca. 5.0 kJ/mol more stable than the hydrogen-bonded rotamer (conformer II) and ca. 2.3 kJ/mol more stable than conformer III. The best agreement with the theoretical calculations is found in the MP2 calculations, which predict conformer I to be 5.1 kJ/mol more stable than III and 1.7 kJ/mol more stable than II.

An Exhaustive Conformational Analysis ofN-Acetyl-l-cysteine-N-methylamide. Identification of the Complete Set of Interconversion Pathways on the ab Initio and DFT Potential Energy Hypersurface

The full conformational space of N-acetyl-l-cysteine-N-methylamide was explored by ab initio (RHF/ 6-31G(d)) and DFT (B3LYP/6-31G(d)) computations. Multidimensional conformational analysis predicts 81 structures in N-acetyl-l-cysteine-N-methylamide, but only 47 relaxed structures were previously determined at the RHF/3-21G level of theory. These structures were now optimized using RHF/6-31G(d) and B3LYP/6-31G(d) approaches. Seven conformational migrations were observed when recalculated at higher level of theory. Besides these major changes, only smaller conformational shifts were operative for the remaining stationary points. The exploration of the whole conformational space of N-acetyl-l-cysteine-N-methylamide, including the transition-state structures allowing the conformational interconversion among the low-energy forms, was analyzed in this study. Our results offer new insights into the influence of polar side chains on the conformational preferences of peptide structures.