Non-adiabatic direct quantum dynamics using force fields: Toward solvation.

Quantum dynamics simulations are becoming a powerful tool for understanding photo-excited molecules. Their poor scaling, however, means that it is hard to study molecules with more than a few atoms accurately, and a major challenge at the moment is the inclusion of the molecular environment. Here, we present a proof of principle for a way to break the two bottlenecks preventing large but accurate simulations. First, the problem of providing the potential energy surfaces for a general system is addressed by parameterizing a standard force field to reproduce the potential surfaces of the molecule's excited-states, including the all-important vibronic coupling. While not shown here, this would trivially enable the use of an explicit solvent. Second, to help the scaling of the nuclear dynamics propagation, a hierarchy of approximations is introduced to the variational multi-configurational Gaussian method that retains the variational quantum wavepacket description of the key quantum degrees of freedom and uses classical trajectories for the remaining in a quantum mechanics/molecular mechanics like approach. The method is referred to as force field quantum dynamics (FF-QD), and a two-state ππ*/nπ* model of uracil, excited to its lowest bright ππ* state, is used as a test case.

Mixed-quantum-classical or fully-quantized dynamics? A unified code to compare methods.

Three methods for non-adiabatic dynamics are compared to highlight their capabilities. Multi-configurational time-dependent Hartree is a full grid-based solution to the time-dependent Schrödinger equation, variational multi-configurational Gaussian (vMCG) uses a less flexible but unrestricted Gaussian wavepacket basis, and trajectory surface hopping (TSH) replaces the nuclear wavepacket with a swarm of classical trajectories. Calculations with all methods using a model Hamiltonian were performed. The vMCG and TSH were also then run in a direct dynamics mode, with the potential energy surfaces calculated on-the-fly using quantum chemistry calculations. All dynamics calculations used the Quantics package, with the TSH calculations using a new interface to a surface hopping code. A novel approach to calculate adiabatic populations from grid-based quantum dynamics using a time-dependent discrete variable representation is presented, allowing a proper comparison of methods. This article is part of the theme issue 'Chemistry without the Born-Oppenheimer approximation'.

Health, physiology, and behavior of dairy calves reared on 4 different substrates.

The objective of this study was to compare the health, physiology, and behavior of group-housed calves reared on wood shavings with those reared on alternative surfaces. At 1 wk of age, 80 calves were moved into 1 of 20 experimental pens (n = 4 calves/pen) where they remained until 6 wk of age. Pens had floors covered with pea gravel (PG), rubber chip (RC), sand (SA), or wood shavings (WS; n = 5 pens/substrate). Body weight, cleanliness, health, and skin surface and vaginal temperature were recorded at 1, 3, and 6 wk of age. Escherichia coli numbers were assessed on the skin surface of the shoulder and in the feces of calves at 3 and 6 wk of age. Blood samples were taken at 1, 3, and 6 wk of age to measure hematological values and cortisol, IgG, and lactate concentrations. Behaviors (lying, running, and self-grooming) were recorded in the home pen at 1, 3, and 6 wk of age using video recorders and accelerometer data loggers. At 6 wk of age, calves were tested individually in an arena test and behavior was recorded continuously for 20 min. Body weight did not differ among calves reared on PG, RC, SA, or WS, regardless of age. All calves were clean and no calves displayed any signs of lameness, leg lesions, or injuries at wk 1, 3, or 6, regardless of substrate. The number of E. coli recovered from a surface area of 100 cm2 on the shoulder of each calf was affected by rearing substrate, with more E. coli recovered from calves reared on WS than PG, RC, or SA at 3 and 6 wk of age. Fecal E. coli counts were not affected by rearing substrate at 3 or 6 wk of age. Over the entire study period, calves reared on PG and SA had lower skin temperatures than calves reared on RC or WS, but skin temperature was similar between calves reared on PG and SA. However, vaginal temperature did not differ among calves reared on different substrates at 1, 3, or 6 wk of age. Hematology values and cortisol, IgG, and lactate concentrations of calves were similar among rearing substrates over the 6-wk study period. In the home pen, rearing substrate did not influence time spent lying; however, calves reared on WS performed more lying bouts than calves reared on PG or SA. In addition, rearing substrate did not influence the time calves spent running; however, calves reared on WS spent more time self-grooming than calves reared on PG, RC, and SA. During a 20-min arena test, running, bucks, jumps, and kicks performed by calves was not affected by rearing substrate. In conclusion, the physiology and behavior of calves reared on PG, RC, and SA was similar to WS, which is considered the preferred rearing substrate to use when rearing calves. Therefore, PG, RC, and SA may be acceptable substrate options when rearing group-housed dairy calves.

Two-dimensional vibronic spectroscopy of molecular aggregates: Trimers, dimers, and monomers.

The two-dimensional (2D) vibronic spectroscopy of molecular trimers is studied theoretically. The solution of the time-dependent Schrödinger equation is carried out with the multi-configurational time-dependent Hartree (MCTDH) method which allows for an efficient propagation of the multi-component wave functions. 2D-spectra are calculated for H- and J-type aggregates incorporating one or two vibrational modes for each monomer. In performing calculations for monomer, dimer, and trimer systems, it is documented how the vibronic structure of the 2D-spectrum changes upon aggregation. This is of importance for the characterization of aggregation behavior being influenced by experimental conditions such as temperature or concentration.

Conformer-resolved quantum dynamics study of the photodissociation of 3-pyrroline.

A model Hamiltonian based on the vibronic coupling model is developed to describe the excited state dynamics of 3-pyrroline. With the use of the method of improved relaxation in conjunction with the MCTDH wavepacket propagation algorithm, vibrational eigenstates corresponding to both the axial and equatorial conformers of 3-pyrroline are calculated and subsequently used in a conformer-resolved study of the photodissociation of 3-pyrroline following excitation to its S1(3s/πσ*) and S2(3px) states. In analogy with ammonia, the excited state dynamics of both conformers of 3-pyrroline are found to be dominated by the (quasi-) planarization of the molecule in its electronically excited states and predominantly diabatic behavior of dissociation mediated by a conical intersection between the S1 and S0 states.

A reinterpretation of the electronic spectrum of pyrrole: a quantum dynamics study.

The first band in the electronic spectrum of pyrrole is calculated from wavepacket propagations performed using the MCTDH method. To do so, two model Hamiltonians are constructed to describe seven low-lying excited electronic states of pyrrole. These Hamiltonians are based on the vibronic coupling model, and are parameterised via fitting to extensive CASPT2 and EOM-CCSD calculations. A detailed analysis of the structure of pyrrole's electronic spectrum in the range 5.5 to 6.5 eV is made. The role of intensity borrowing from transitions to ππ(*) states by lower-lying 3s and 3p Rydberg states is assessed, and reassignments of much of the spectrum are subsequently made which indicate that most of the states in the spectrum are predominantly Rydberg in character. The resulting conclusions drawn serve to highlight the limitations of assignments based on the matching of calculated vertical excitation energies and the positions of peak maxima observed in electronic spectra.

The effect of rearing substrate and space allowance on the behavior and physiology of dairy calves.

The objective of this study was to investigate the effect of rearing substrate and space allowance on the behavior and physiology of dairy calves. At 1 wk of age, 72 calves were moved into 1 of 18 experimental pens (n=4 calves/pen) where they remained until 6 wk of age. Half of the pens had floors covered with quarry stones (QS) and the other half were covered with sawdust (SW). For each substrate type, calves were reared at 1 of 3 space allowances: 1.0, 1.5, or 2.0 m(2)/calf. Behavior was video-recorded continuously for 24 h in the home pen at 2, 4, and 6 wk of age; the time calves spent lying, standing, walking, and running were estimated using 1-min instantaneous scan sampling. Body weight, cleanliness, fecal fluidity, and skin surface temperature were recorded at 1, 4, and 6 wk of age. Escherichia coli numbers were assessed on the skin surface of the shoulder and in feces of calves at 4 and 6 wk of age. Blood samples were taken at 1, 4, and 6 wk of age to measure cortisol, creatine kinase, immunoglobulin G, serum amyloid A, and total protein concentrations. Calves reared on QS spent less time lying and walking and more time standing at 4 and 6 wk of age compared with calves reared on SW. Furthermore, calves reared at a space allowance of 2.0 m(2)/calf spent less time lying and more time standing and walking compared with calves reared at a space allowance of 1.0 and 1.5 m(2)/calf. Calves reared on QS had lower skin surface temperatures compared with calves reared on SW. Fecal fluidity scores were lower in calves reared on QS than SW at 2 wk of age. Fewer E. coli were recovered from the shoulder of calves reared on QS than those of calves reared on SW, but fecal E. coli counts were similar between rearing substrates and space allowances. Serum amyloid A concentrations were lower in calves reared on QS than SW. We detected no effect of rearing substrate or space allowance on body weight, cleanliness, or concentrations of cortisol, creatine kinase, immunoglobulin G, and total protein. In conclusion, lower skin temperature in combination with reduced lying behavior may reflect reduced comfort of calves reared on QS. Furthermore, a space allowance of 2.0 m(2)/calf may provide calves with more opportunity to perform active behaviors.

Quantum dynamics study of photoexcited aniline.

A model Hamiltonian based on the quadratic vibronic coupling model is developed to describe the photoinduced dynamics of aniline excited to the manifold of states comprising its first six singlet electronic states. The model Hamiltonian is parametrized by fitting to the results of extensive EOM-CCSD calculations and its validity tested through the calculation of the first two bands in the electronic absorption spectrum of aniline. It is found that two previously neglected 3p Rydberg states play an important role in the dynamics of aniline following excitation into the first two (1)ππ* states. Assignments of the vibrational structure seen in the experimental spectrum is made, and the role played by the Herzberg-Teller effect in excitation to the first (1)ππ* state is analyzed.

Quantum dynamics study of the competing ultrafast intersystem crossing and internal conversion in the "channel 3" region of benzene.

Time-resolved photoelectron spectroscopy can obtain detailed information about the dynamics of a chemical process on the femtosecond timescale. The resulting signal from such detailed experiments is often difficult to analyze and therefore theoretical calculations are important in providing support. In this paper we continue our work on the competing pathways in the photophysics and photochemistry of benzene after excitation into the "channel 3" region [R. S. Minns, D. S. N. Parker, T. J. Penfold, G. A. Worth, and H. H. Fielding, Phys. Chem. Chem. Phys. 12, 15607 (2010)] with details of the calculations shown previously, building on a vibronic coupling Hamiltonian [T. J. Penfold and G. A. Worth, J. Chem. Phys. 131, 064303 (2009)] to include the triplet manifold. New experimental data are also presented suggesting that an oscillatory signal is due to a hot band excitation. The experiments show that signals are obtained from three regions of the potential surfaces, three open channels, which are assigned with the help of simulations showing that following excitation into vibrationally excited-states of S(1) the wavepacket not only crosses through the prefulvenoid conical intersection back to the singlet ground state, but also undergoes ultrafast intersystem crossing to low lying triplet states. The model is, however, not detailed enough to capture the full details of the oscillatory signal due to the hot band.

The clinical and economic burden after an osteoporosis fracture in France: a nationwide population-based study.

Osteoporosis-related fragility fractures increase the risk of subsequent fractures and are associated with substantial morbidity and mortality. Emphasis should be placed on the prevention of recurrent fractures, which will decrease both the clinical burden on patients and the economic burden on the health system. INTRODUCTION: Fragility fractures are associated with increased morbidity and mortality. Quantifying the clinical and economic burden of subsequent fractures following an initial osteoporosis-related fracture is a key to informing public health policies. METHODS: A retrospective cohort study, using the national French health insurance claims database. Males and females ≥ 50 years, with a hospital discharge diagnosis of osteoporosis with fracture or a relevant fragility fracture (hip, vertebrae, femur, pelvis, wrist/hand, forearm, humerus/clavicle) between 2011 and 2014, were included and followed until death or end of 2016, whichever came first. Index fracture was the first qualifying hospitalization; subsequent fractures were defined as those occurring either at a different site from the index fracture or at the same site ≥ 90 days apart. Costs abstracted included hospitalization, external consultation, outpatient visits, and treatment. RESULTS: A total of 544,426 participants (132,148 [24.3%] males and 412,278 [75.7%] females), of whom 16,110 (12.2%) males and 73,538 (17.8%) females had at least one subsequent fracture during follow-up, were included. Incidence of subsequent fracture was highest in the first year following index fracture. During follow-up, 161,179 patients died; mortality was highest among those with a hip fracture at index (29,971 (51.6%) males and 65,254 (39.6%) females). Total mean costs per patient in the year following index fracture were highest for males and females with a hip fracture (€18,585 and €15,754, respectively). CONCLUSION: Subsequent fractures among osteoporotic participants with an initial fracture result in increased clinical mortality and high healthcare resource use. Emphasis should be placed on the prevention of recurrent fractures.

Local control of multidimensional dynamics.

The control of chemical reactions has been a target for researchers since the development of lasers which operated on a timescale fast enough to follow nuclear motion. Since then a number of schemes have been developed, each proving successful in a selection of systems. In this paper we present results obtained following the implementation of local control theory together with the multi-configuration time dependent Hartree quantum dynamics algorithm, aiming to efficiently design control pulses for polyatomic systems. Control of multidimensional models of cyclobutadiene and pyrazine are presented and discussed. These results represent a starting point for further studies, showing the distinct advantages of using this approach for controlling chemical reactions.

Competing ultrafast intersystem crossing and internal conversion in the "channel 3" region of benzene.

We report new, detailed, femtosecond time-resolved photoelectron spectroscopy experiments and calculations investigating the competition between ultrafast internal conversion and ultrafast intersystem crossing in electronically and vibrationally excited benzene at the onset of "channel 3". Using different probe energies to record the total photoelectron yield as a function of pump-probe delay we are able to confirm that S(1), T(1) and T(2) electronic states are involved in the excited state dynamics. Time-resolved photoelectron spectroscopy measurements then allow us to unravel the evolution of the S(1), T(1) and T(2) components of the excited state population and, together with complementary quantum chemistry and quantum dynamics calculations, support our earlier proposal that ultrafast intersystem crossing competes with internal conversion (Chem. Phys. Lett., 2009, 469, 43).

Multimode quantum dynamics using Gaussian wavepackets: The Gaussian-based multiconfiguration time-dependent Hartree (G-MCTDH) method applied to the absorption spectrum of pyrazine.

The Gaussian-based multiconfiguration time-dependent Hartree (G-MCTDH) method is applied to calculate the S(2)(pipi( *)) absorption spectrum of the pyrazine molecule, whose diffuse structure results from the ultrafast nonadiabatic dynamics at the S(2)-S(1) conical intersection. The 24-mode second-order vibronic-coupling model of Raab et al. [J. Chem. Phys. 110, 936 (1999)] is employed, along with 4-mode and 10-mode reduced-dimensional variants of this model. G-MCTDH can be used either as an all-Gaussian approach or else as a hybrid method using a partitioning into primary modes, treated by conventional MCTDH basis functions, and secondary modes described by Gaussian particles. Comparison with standard MCTDH calculations shows that the method converges to the exact result. The variational, nonclassical evolution of the moving Gaussian basis is a key element in obtaining convergence. For high-dimensional systems, convergence is significantly accelerated if the method is employed as a hybrid scheme.

Effect of pre-slaughter handling, exercise and the presence of a dog on lamb welfare and meat quality.

Before slaughter, lambs may experience several stressors such as feed and water deprivation, handling and transport that have the potential to negatively impact welfare and meat quality. The objective of this study was to evaluate the effect of pre-slaughter handling, exercise and the presence of a dog on the behaviour and physiology of lambs and meat quality at slaughter. At 6 months of age, 60 lambs (n=20 lambs/replicate; three replicates) were allocated to one of the two treatment groups (n=30 lambs/treatment): low (LOW) intensive handling or high (HIGH) intensive handling. LOW lambs were moved short distances, quietly and without the use of a dog before transport. HIGH lambs were moved quickly, long distances and with a dog present before transport. Lamb behaviour (standing, lying, rumination and panting) was recorded for 1 h before (post-treatment) and after transport (post-transport), and for 30 min before slaughter (pre-slaughter). Blood samples were collected before (baseline), after transport (post-transport) and at exsanguination (at slaughter) to assess cortisol, lactate and non-esterified fatty acid (NEFA) concentrations. At slaughter, lamb carcases (M. longissimus lumborum) were evaluated for pH levels, drip and cook loss, and tenderness. HIGH lambs spent more time standing (P<0.001) and panting (P<0.001) and less time lying (P<0.001) and ruminating (P<0.001) post-treatment than LOW lambs, but more (P<0.001) time ruminating post-transport. All lambs spent more time standing (P<0.001) and less time lying (P<0.001) and panting (P<0.001) post-transport and pre-slaughter than post-treatment. Cortisol concentrations were greater (P<0.001) in lambs post-transport and at slaughter compared with baseline values. Lactate concentrations were lower (P=0.002) in HIGH than LOW lambs. In addition, NEFA concentrations were higher (P<0.001) post-transport and at slaughter in HIGH compared with LOW lambs. Ultimate pH was higher (P<0.001) in HIGH than LOW lambs and pH declined quicker (P=0.012) in LOW than HIGH lambs. Cook loss, drip loss and shear force were lower (P⩽0.05) in HIGH than LOW lambs. The HIGH intensive pre-slaughter handling regime used in the present study caused stress in lambs and increased ultimate pH that could potentially negatively impact welfare, product quality and consistency.

Histamine tautomerism and its mode of action.

An established combination of quantum mechanical calculations and molecular dynamics simulations (Worth, C.A., King, P.M. and Richards, W.G. (1989) Biochim. Biophys. Acta 993, 134-136; Cieplak, P., Singh, U.C. and Kollman, P.A. (1987) Int. J. Quant. Chem. QBS14, 65-74; Reynolds, C.A., King, P.M. and Richards, W.G. (1988) Nature 334, 80-82) has been used to calculate the tautomer ratios of histamine species in aqueous solution. The results are in good agreement with experiment and provide a bridge between experimental data and earlier theoretical calculations.

Theoretical calculation of tautomer equilibria in solution: 4-(5-)methylimidazole.

A combination of quantum mechanical calculations and molecular dynamics simulations has been used to calculate the tautomer ratio of 4-(5-)methyl imidazole in solution, and the results are in good agreement with experiment.

Alterations in vitamin D metabolites during treatment of Paget's disease of bone with calcitonin or etidronate.

We report serum 25-hydroxyvitamin D (25-OHD), 24,25-dihydroxyvitamin D [24,25-(OH)2D], and 1,25-dihydroxyvitamin D [1,25-(OH)2D] levels in untreated Paget's disease and the effect of treatment with either calcitonin (CT) or etidronate (EHDP) on these levels. In untreated Paget's patients serum 25-OHD (73 +/- 29 nmol/liter, n = 36, mean +/- SD) and 24,25-(OH)2D (0.3-12.9 nmol/liter, median 2.2, n = 36) levels were significantly lower than in age-matched controls (94 +/- 30 nmol/liter, n = 32, p less than 0.005, and 1.3-16.4 nmol/liter, median 5.3; n = 32, p less than 0.001, respectively). Also, the 24,25-(OH)2D levels correlated with the 25-OHD levels in the untreated Paget's patients (r = 0.56, p less than 0.01) and in the controls (r = 0.39, p less than 0.05). The percentage molar ratio of 24,25-(OH)2D to 25-OHD in Paget's patients had a median value of 3.7% (range 0.4-14.3%), which was not significantly different from controls, who had a median value of 5.6% (range 2.2-18%). There was no difference between the 1,25-(OH)2D, and immunoreactive PTH (iPTH) levels of Paget's patients and control subjects. The percentage molar ratio of 1,25-(OH)2D to 25-OHD in untreated Paget's patients (0.157 +/- 0.09%) was not significantly different from controls (0.124 +/- 0.05%) despite lower 25-OHD levels in Paget's patients. There was a significant inverse correlation between the severity of Paget's disease as measured by plasma alkaline phosphatase (AP) levels and 25-OHD levels (r = 0.392, p less than 0.02); however, 24,25-(OH)2D and 1,25-(OH)2D levels were not correlated with AP.(ABSTRACT TRUNCATED AT 250 WORDS)

Long-term elevation of 1,25-dihydroxyvitamin D after short-term intravenous administration of pamidronate (aminohydroxypropylidene bisphosphonate, APD) in Paget's disease of bone.

We report the prolonged biochemical changes that occurred in patients with Paget's disease when treated for 2-10 days with pamidronate disodium (3-amino-1-hydroxypropylidine-1,1-bisphosphonate, APD), by i.v. administration and observed for 6 months following therapy. In all 24 patients studied, bone resorption (measured by urinary hydroxyproline/creatinine ratio, OHP/Cr) fell sharply on treatment, from 0.12 +/- 0.02 (mean +/- SEM; above reference limits) to 0.04 +/- 0.008 (reference range 0.006-0.027 for females, 0.005-0.020 for males), remaining at this level for 6 months after therapy. A fall in serum ionized calcium (Ca2+) to just below the reference limits with treatment (1.11 +/- 0.02 mM; reference range 1.14-1.18 mM), followed by a rapid return to normal levels (1.14 +/- 0.02 mM, mean +/- SEM) within 8 days of treatment, was presumably due to the cessation of release of calcium from bone. This was followed by secondary hyperparathyroidism and a rise in serum 1,25-dihydroxyvitamin D [1,25(OH)2D]. The hormonal responses, however, were profound. Serum immunoreactive PTH (iPTH) rose to twice pretreatment values (86 +/- 11 pM, mean +/- SEM; reference range for iPTH, > 50 years, < 50 pM; < 50 years, < 40 pM), returning to normal 4-8 weeks after therapy. Serum 1,25-(OH)2D levels rose to three times pretreatment values (300 +/- 20 pM, mean +/- SEM; reference range 50-150 pM), remaining above reference limits 4-8 weeks after therapy (188 +/- 15 pM, mean +/- SEM) and returning to normal values only after 12 weeks.(ABSTRACT TRUNCATED AT 250 WORDS)