bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of unusually early visual stimulation on the development of homing behavior in the rat pup
Authors: Kenny Patricia A. , Turkewitz Gerald
Published: January 2005

Two studies examined the theory that early limitations on sensory functioning contribute to the organization of a structure for perceptual development and intersensory functioning. Rat pups' eyelids were surgically opened on Day 7, following which the development of homing to their nest site was investigated, with each animal alone in its living cage. Control pups increased homing until Day 14, and then decreased. Experimental pups showed no such decline, with the highest rate of homing evident on the last day of testing. The importance of visual cues for this altered development of homing was examined. Visual cues for the home were reduced by removing all shavings during testing, while leaving an odorous substrate in place. Under these conditions, both groups showed the characteristic increase and decline in homing, suggesting that premature eyelid opening results in a modification of the distribution of attention to visual and olfactory characteristics of the nest.
Impoverished rearing conditions increase stress‐induced irritability in mice
Authors: Riittinen M.‐L. , Lindroos F. , Kimanen A. , Pieninkeroinen E. , Pieninkeroinen I. , Sippola J. , Veilahti J. , Bergström M. , Johansson G.
Published: January 2005

Irritability was tested in mice reared in four environmental conditions: impoverished (IC), impoverished + overstimulated (ICS), enriched (EC), and enriched + overstimulated (ECS) conditions. The test used was a modified “bottle brush” test. Both overstimulations and individual housing increased irritability interacting positively with each other. Individual housing but not overstimulation decreased avoidance behavior in the mice.
Sex‐related behavior of immature wild mountain gorillas
Authors: Nadler Ronald D.
Published: January 2005

Sex‐related behavior in immature wild mountain gorillas consisted primarily of gental stimulating episodes in which one animal thrusted against the body of another. Whereas the immature males used the D‐V position predominantly, a single immature female that performed as an actor used the V‐V position exclusively. All episodes of genital stimulating behavior originated in the context of play and most actors were older (and larger) than recipients of such behavior. The data support the findings of earlier research but suggest that genital stimulating behavior among immature gorillas occurs more frequently than previously thought. These results in conjunction with comparable data on pygmy and common chimpanzees and orangutans suggest that genital‐stimulating behavior by immature individuals is a species‐typical phenomenon in the behavioral development of the great apes.
Social interactions among rats housed in grouped and enriched conditions
Authors: Renner Michael J. , Rosenzweig Mark R.
Published: January 2005

Two experiments examine the hypothesis that brain differences found in environmental enrichment are due to differences in social interaction. Both experiments compare enriched versus group housed rats using videotape records of home cage activity, scored with a protocol developed by the authors. Experiment 1 examines social interactions in group and enriched housed rats in the first 30 days postweaning; In Experiment 2 rats were housed in the differential environments from 90 to 120 days of age, an age at which rats have been reported no longer to engage in play; in addition, weights of sections of the brain were obtained at sacrifice and these showed typical patterns of differences among rats from differential environments. Neither experiment revealed any consistent pattern of differences in social interaction, either by chi‐square comparisons of overall profiles of social activity or by discriminant analysis applied to behavioral observations. No evidence was found in support of the hypothesis that play is responsible for the effects of environmental enrichment.
Discrimination between conspecific and allospecific infants by male gerbils and mice before and after experience of their own young
Authors: Elwood Robert W. , Ostermeyer Malcolm C.
Published: January 2005

Prior to the birth of their 1st litter, male gerbils generally respond paternally toward both gerbil and mouse pups. Once they have experience of their own pups, however, they continue to respond paternally toward unrelated gerbil pups but kill mouse pups. Male CSI mice, on the other hand, respond paternally to unrelated mouse pups both before and after the birth of their own litter but tend to ignore gerbil pups at these times. These data are discussed with respect to infanticide, onset of paternal care and the narrowing of effective stimuli for eliciting paternal care.
Rhythmic organization of the sound of infant crying
Authors: Zeskind Philip Sanford , Parker‐Price Susan , Barr Ronald G.
Published: January 2005

The purpose of the present study was to examine the temporal morphology and rhythmic structure underlying the repeated bursts of expiratory sounds in a sustained bout of crying of twenty‐three 1‐month‐old infants. Durations of expiratory sounds and bursts were determined from a 90‐s bout of naturally occurring cries recorded in the home before feeding. Results indicated wide individual differences in temporal morphology between infants and within infant cry sounds. Binary spectrum analysis of the presence of expiratory sounds in the cry sound detected rhythms in temporal organization at a wide range of dominant frequencies. Spectral complexity (higher numbers of peaks in the power spectrum) was related to a longer time since infants were last fed and shorter expiratory sounds. Results emphasize the importance of viewing cries of young infants as dynamic signals. An ontogenetic history of the rhythms of infant cry sounds may contribute to understanding organismic and environmental experiences which contribute to development. © 1993 John Wiley & Sons, Inc.
Responses to ecologically relevant stimuli in the rat fetus: Interactive effects of milk and an artificial nipple
Authors: Smotherman William P. , Arnold H. Moore , Robinson Scott R.
Published: January 2005

Stimuli normally encountered during suckling after birth—the nipple and milk—elicit behavioral responses from fat fetuses on E20. A series of experiments demonstrated that milk, unlike other chemosensory stimuli, consistently evoked mouthing activity during the 15 s after presentation. Unlike other perioral tactile stimuli, an artificial nipple evoked mouthing activity and an active oral grasping response during presentation. Prior exposure to milk altered fetal responsiveness to some forms of perioral tactile stimulation, but did not affect grasping of the nipple. In contrast, prior exposure to an artificial nipple increased mouthing activity in response to milk. The nipple and milk exhibit a temporally asymmetric relationship in fetal rats, which lack experience with suckling stimuli. These findings suggest that responsiveness to ecologically relevant stimuli and their temporal presentation develops before birth, and may facilitate functional behavioral responses of the newborn during the first suckling episode. © 1993 John Wiley & Sons, Inc.
Beer, breast feeding, and folklore
Authors: Mennella Julie A. , Beauchamp Gary K.
Published: January 2005

Beer consumption by nursing women altered the sensory qualities of their milk and the behavior of their infants during breast‐feeding in the short term. The infants consumed significantly less milk during the 4‐hr testing sessions in which their mothers drank alcoholic beer compared to when the mothers drank nonalcoholic beer; this decrease in milk intake was not due to a decrease in the number of times the babies fed. Although the infants consumed less of the alcohol‐flavored milk, the mothers believed their infants had ingested enough milk, reported that they experienced a letdown during nursing, and felt they had milk remaining in their breasts at the end of the majority of feedings. Moreover, the mothers terminated the feeds the same percentage of time on both testing days. The mechanism by which the consumption of alcoholic beer by lactating women decreases milk intake by their nurslings remains to be determined. © 1993 John Wiley & Sons Inc.
Robustness of individual identity in the cries of human infants
Authors: Gustafson Gwen E. , Green James A. , Cleland Jerry W.
Published: January 2005

This study investigated the possibility that one function of the human infant's cry is to convey individual identity across distance. Six‐hundred adults, having been exposed to 30 s of an infant's crying, were asked to identify this infant on the basis of other, experimentally altered, cries. The cries were altered naturally by rerecording across distance in the out‐of‐doors, and artificially by bandpass filtering and temporal reorganization. The individuality of cries proved remarkably robust to degradation: Only when frequencies were limited to the range of 8 to 10 kHz was recognition performance significantly impaired. It is argued that the human infant's cry, a complex signal with multiple markers of individuality, may have among its functions the communication of infants' identities across distance.© 1994 John Wiley & Sons, Inc.
Effects of CCK‐8 on ingestive behaviors of suckling and weanling rats
Authors: Lorenz Dennis N.
Published: January 2005

The present series of experiments was designed to determine the dose—response characteristics of the cholecystokinin suppression effect on rat pups ingesting through suckling and adult modes. Pups at 10–22 days of age were deprived of their dam and food for 6 hr. At test time, the subjects received intraperitoneal injections or intravenous infusions of CCK‐8 at 2, 4, 8, or 16 μg/kg in saline, or the saline vehicle alone. The pups were permitted to ingest for 30 min immediately after the injection or during the infusion. Ingestion included taking milk from the dam by suckling or feeding from the substrate. Regardless of the route of administration, CCK‐8 elicited a low level of suppression across all doses and all ages when pups ingested within the natural suckling situation. In marked contrast, pups ingesting from the substrate in the adult mode suppressed their intake of bovine light cream or chow pellets in a dose‐related manner following injections of the peptide. The blockade of the CCK dose‐related suppression effect during suckling indicates that a different set of mechanisms governs intake of milk from the mother. The results may be related to the level of arousal required to sustain motivated behaviors while pups engage in the different modes of ingestion.© 1994 John Wiley & Sons, Inc.
Ontogeny of context‐specific latent inhibition of conditioned fear: Implications for configural associations theory and hippocampal formation development
Authors: Rudy Jerry W.
Published: January 2005

Latent inhibition of fear conditioning to an auditory cue, as measured by behavioral freezing, was examined in 18‐ and 23‐day‐old rats. In Experiment 1, CS preexposure and conditioning occurred in the same context for some rats but in a different context for other rats, and 24 hr separated CS preexposure and conditioning. The 23‐day‐old rats showed a context‐specific latent inhibition effect, but the 18‐day‐old rats showed no latent inhibition. In Experiment 2, CS preexposure and conditioning occurred in the same trainining session and both 18‐ and 23‐day‐old rats showed latent inhibition. These results were discussed in relation to Wagner's (1976) theory of information processing, hippocampal formation maturation, and function, and Sutherland and Rudy's (1989) configural association theory.©1994 John Wiley & Sons, Inc.
Vagal tone during quiet sleep in normal human term fetuses
Authors: Groome Lynn J. , Mooney Donna M. , Bentz Lynn S. , Doug Wilson J.
Published: January 2005

The purpose of this paper was to calculate vagal tone (V) for 17 normal human fetuses in quiet sleep (QS) between 36 and 40 weeks gestation. The fetal cardiac electrical signal was captured transabdominally in 3‐min blocks at a rate of 833 times per second and fetal R‐waves were extracted using adaptive signal processing techniques. Fetal R‐wave interbeat intervals were converted to equally spaced, time‐based data, and the low‐frequency component was removed using a 21‐point third‐order moving polynomial. The parameter V was calculated by taking the natural logarithm of the sum of the power densities between 0.3 Hz and 1.3 Hz. We found that fetal breathing was associated with an approximately 25% increase in V as compared to nonbreathing, 3.33 ± 0.48 versus 2.57 The Official Journal of the International Society for Developmental Psychobiology 0.47, p < 0.0001. Furthermore, there was a significant linear relationship between the mean single‐fetus V during spontaneous respiration and the mean single‐fetus V during normally occurring apneic periods, r = 0.772, p < 0.002. We conclude that respiratory activity is associated with a significant increase in vagal tone for normal human fetuses in QS.©1994 John Wiley & Sons, Inc.
On the importance of evolution to developmental psychobiology
Authors: Hill Wendy L.
Published: January 2005

The termdevelpomental psychobiologyimplies an integration between psychology and biology. But what segment of biology does the discipline embrace? The present commentary asserts that developmental psychobiology devotes too much attention to structural biology, with its emphasis on proximate mechanisms, and fails to give enough prominence to evolutionary biology and ultimate perspectives. I have attempted to portray the significance of evolution to developmental psychobiology and to elaborate on how developmental psychobiology might contribute to refinements in evolutionary theory, especially recent modifications that advocate a greater role for developmental processes. Methodological suggestions are offered, which would broaden developmental psychobiology's perspective so that a more comprehensive analysis of behavioral development results. © 1995 John Wiley & Sons, Inc.
Salivary cortisol in nursery‐reared rhesus monkeys: Reactivity to peer interactions and altered circadian activity
Authors: Thomas Boyce W. , Champoux Maribeth , Suomi Stephen J. , Gunnar Megan R.
Published: January 2005

Five nursery‐reared rhesus (Macaca mulatta) infants were studied on 8 consecutive days over a period of 2 weeks when they ranged from 4 to 5.5 months. Saliva cortisol samples were obtained by giving each animal, while in its individual home cage, a 6‐in. cotton dental roll pretreated with sugared fruit‐drink crystals and dried. Subjects were allowed to mouth the cotton roll for 10 min during each collection period. Saliva was then expressed from the cotton and analyzed by radioimmune assay. Samples were collected at 0830, 1100, 1400, and 1630 hr on each of the 8 days. On four of the days, 2‐hr peer socialization sessions were imposed between 1200 and 1400 hr. Significant time‐of‐day effects were obtained. Values tended to be low at 0830 hr, rising significantly to peak levels at 1100 hr, and then declining over the 1400‐hr and 1630‐hr sampling periods. All 4 subjects with sufficient samples had higher average cortisol concentrations when the 1400‐hr sampling followed peer‐socialization sessions, compared to no‐socialization days. This difference was only marginally significant by paired t test, however. These results (a) support the feasibility of using noninvasive salivary sampling procedures with infant monkeys, and (b) indicate that salivary cortisol measures are sensitive to daily rhythms. Unexpectedly, the results also raise the possibility that nursery‐reared infant rhesus macaques may be phase‐delayed in their HPA rhythm, with the morning peak occurring several hours after rather than in the hour before lights‐on and the morning feeding. © 1995 John Wiley & Sons, Inc.
The inhibition of automatic saccades in early infancy
Authors: Johnson Mark H.
Published: January 2005

Adult patients with damage centered around the frontal eye fields are severely impaired in the ability to suppress unwanted automatic saccades and in the ability to make volitional eye movements. Over the first few weeks of life most saccades generated by infants appear to be automatic, and are triggered in response to exogenous factors. In the first experiment, the ability of 4‐month‐old infants to inhibit automatic saccades was studied by exposing them to a series of trials in which a peripheral cue stimulus predicted the location (opposite) in which a colorful, dynamic target stimulus appeared. The results indicate that 4‐month‐old infants are able to learn to inhibit automatic saccades to a peripheral stimulus, implying maturation of the frontal eye fields by this age. The results of Experiment 2, in which there was no contingent relationship between the cue and target, indicated that the decline in orienting to the cue observed in the first experiment was not due to differential habituation to the less‐complex stimulus. © 1995 John Wiley & Sons, Inc.
Prenatal stress alters immune function in the offspring of rats
Authors: Klein Sabra L. , Rager Dawn R.
Published: January 2005

Pregnant rats were either exposed to restraint under bright lights for 45 min three times daily (n = 7) or were left undisturbed (n = 8) during Days 14–21 of gestation. Offspring were tested for cellular immune responses as measured by Concanavalin A‐stimulated proliferation and Natural Killer (NK) cytotoxicity of splenocytes as juveniles or adults, or were tested for specific humoral immune responses to in vivo challenge with the antigen Keyhole Limpet Hemocyanin (KLH) as adults. Results indicated that: (a) Proliferation did not vary as a function of sex or prenatal treatment in either juvenile or adult offspring; (b) in juveniles NK cytotoxicity was marginally lower in males as compared to females, and was also marginally reduced by prenatal stress in males but not females, whereas in adults, NK cytotoxicity was marginally enhanced by prenatal stress in both sexes; and (c) prenatally stressed offspring of both sexes had higher levels of anti‐KLH antibodies as compared to controls. © 1995 Johnv Wiley & Sons, Inc.
On the relative importance of core and valence shell representations in the calculation of conformational energies using small Gaussian basis sets
Authors: Mezey Paul G. , Rao Ch. V. S. Ramachandra
Published: January 2005

Several “core‐deficient” small Gaussian basis sets were constructed and analyzed in terms of the balance requirements of functions that contribute predominantly to the core. Variations in the conformational energy barriers and geometrical parameters for ammonia and ethane, calculated with these basis sets, were analyzed with a gradient technique. A scheme for the reduction of the size of molecular basis sets is proposed.
A note on density matrix extrapolation and multiple solutions of the unrestricted Hartree–Fock equations
Authors: Mezey P. G. , Strausz O. P. , Gosavi R. K.
Published: January 2005

Unrestricted Hartree–Fock (UHF) SCF–MO calculations on the doublet reaction surface for the addition of methylidyne (CH) to ethylene (C2H4) using the standard extrapolation techniques of the GAUSSIAN 70 program show erratic behavior. On the other hand, the potential energy surface calculated without extrapolation of the density matrix and by using the final density matrix of a neighboring point as the initial guess for the density matrix for the new point gave a smooth potential curve without any kinks or erratic pattern. Therefore, the density extrapolation technique should be used with particular caution in UHF calculations.
A systematic preparation of new contracted Gaussian‐type orbital sets. III. Second‐row atoms from Li through ne
Authors: Tatewaki Hiroshi , Huzinaga Sigeru
Published: January 2005

Four minimal Gaussian basis sets are generated for the second‐row atoms Li through Ne. The first one, MINI‐1, consists of a 3‐term contraction of primitive Gaussian‐type orbitals for 1s, 2s, and 2p atomic orbitals. The convenient shorthand notation would be (3,3) for LiBe and (3,3/3) for BNe. The second one, MINI‐2, can be represented by (3,3/4) for BNe. In the same way, MINI‐3 is described as (4,3) for LiBe, and MINI‐3 and MINI‐4 are represented by (4,3/3) and (4,3/4) for BNe, respectively. Although the four basis sets are the minimal type, they give the valence shell orbital energies which are close to those of DZ. These four and other sets derived from them are tested for the hetero‐ and homodiatomic molecules and some organic molecules. They are found to give the orbital energies that agree well with those given by extended calculations. Atomization energies and other spectroscopic constants are also calculated and compared with those of extended calculations. The results clearly indicate that the present basis sets can be used very effectively in the molecular calculations.
The electronic structure and optical activity of conjugated dienes: 1,3‐Butadiene and α‐ and β‐phellandrene
Authors: Rauk Arvi , Peoples H. Allan
Published: January 2005

The optical activity of conjugated dienes is investigated by means of ab initio SCF–CI calculations. The computed electronic spectrum of trans‐1,3‐butadiene is shown to be in good agreement with the results of more rigorous calculations of the valence transitions and in satisfactory agreement with experiment. The optical rotatory strengths of the lower electronic transitions of twisted 1,3‐butadiene as a function of dihedral angle are presented and simulated CD spectra are produced. The N → V1 (π2 → π3*) transition is predicted to have a positive rotational strength for all dihedral angles that correspond to a right‐handed twist of the chromophore, in accord with the empirically deduced “diene rule” although for a twist angle of 60°, the rotatory strength is calculated to be almost zero. The role of the orientation of allylic bonds is investigated in the model system 1‐butene in which the rotational strength of the π → π* transition as a function of rotation about the 2,3 bond is determined. The effect of allylic bond disposition in dienes on the optical activity of the long‐wavelength π2 → π3* transition is simulated by use of the exciton coupling model of Harada and Nakanishi in which two 1‐butene molecules with suitable geometries are coupled via interactions of the electric dipole transition moments of their π → π* transitions. The model systems 1,3‐butadiene and 1‐butene are used to rationalize the apparently anomalous optical activity of (−)‐α‐phellandrene and (−)‐β‐phellandrene, both of which should have a diene chromophore with a right‐handed twist in their most stable conformers and so should be dextrorotatory. The experimental CD spectrum of α‐phellandrene is determined at several temperatures down to −180°C. The observed variation of the apparent rotational strength of the N → V1 transition is in good agreement with that predicted by use of the exciton coupling model.
Ab initio calculations of the rotational potential functions for propylamine and ethylmethylamine
Authors: Allinger Norman L. , Burkert Ulrich , Profeta Salvatore
Published: January 2005

Calculations at the STO‐3G and 4–31G levels have been carried out on propylamine and ethylmethylamine, using geometries determined by molecular mechanics by allowing complete molecular relaxation in all degrees of freedom except for torsion about the central bond, and at 30° increments for the latter. It was found that a butanelike potential exists in each case. From 0° (cis) to 360° in order, the 4–31G values for the energy extrema are 5.92, 0.12, 3.88, 0.00, 3.94, and 0.51 kcal/mole for propylamine (with the nitrogen lone pair gauche to carbon), and 7.06, 1.45, 3.44, 0.0, 2.87, and 1.44 kcal/mole for ethylmethylamine.
An ab initio study of the geometry and energy of six planar conformers of β‐hydroxyacrolein
Authors: George Phillip , Bock Charles W. , Trachtman Mendel
Published: January 2005

Ab initio calculations with full geometry optimization have been carried out on the planar cCc, cTc, tTc, tCt, tTt, and cCt conformers of β‐hydroxyacrolein using the 4‐21G basis set, and on the cCc and cCt conformers using the 4‐31G basis set. The hydrogen‐bonded cCc conformer is the most stable and the cCt conformer the least stable, with the other conformers following the above sequence. β‐Hydroxy substitution has scarcely any influence on the geometry of the trans‐acrolein structure, whereas the geometry of the cis‐acrolein structure shows significant changes which depend on whether the OH group is cis or trans with respect to the CHO group about the CC bond. The ΔET values for cis → trans isomerization about the CC bond in cCt and cTc support the hypothesis that these changes in geometry are the result of a destabilizing interaction in cCt and a stabilizing interaction in cTc. The geometry of the hydrogen‐bonded structure cCc sets it apart from all the other conformers: it has by far the longest CC, the longest CO, the longest OH, the shortest CC, and the shortest CO. Its formation from cCt involves a lengthening of CC, CO, and OH and a shortening of CC and CO, indicating a delocalization of charge within the ring. 4‐21G calculations have also been made for a distorted cCt structure that has the same bond lengths and angles as the equilibrium cCc structure, and the distortion energy, cCt (equm. geom.) → cCt (distorted geom.), is found to be +13.1 kJ mole−1. Taking the energy of this distorted cCt structure as the baseline, the hydrogen‐bonding energy in cCc is found to be —80.3 kJ mole−1.
Random walks and their diagnostic value for characterization of atomic environment
Authors: Randić Milan
Published: January 2005

A characterization of atomic environments based on counting random walks in a molecular skeleton is outlined. To each atom in a molecule a sequence of integers w1, w2, w3,…, wn is assigned, where wi represents the number of self‐returning walks of length k, the length being defined by the number of bonds traversed. Properties of the derived atom codes are discussed. The codes display an impressive diversity and are superior to atomic codes based on enumeration of self‐avoiding walks (or paths) in discriminating atomic environments. In certain cases the codes of individual atoms are not unique and the same codes appear in different molecules or even within the same molecule. The occurrence of the nonunique codes can be related to special structural situations, associated with the occurrence of isospectral graphs. These isospectral graphs which have atoms with identical codes can generate additional isospectral structures by attaching any arbitrary group to such points. If nonequivalent atoms of a single molecule have identical random walk codes, substitution at the singular points alternatively will produce isospectral graphs. Examples of such situations are given.
Quantum chemical investigations of charge transfer interactions in relation to the electronic theory of cancer. IV. The interaction of formamide and the enol tautomers of several glyoxals
Authors: Ball John R. , Thomson Colin
Published: January 2005

The results of ab initio “supermolecule” calculations of the charge transfer between formamide and the enol forms of methylglyoxal, ethylglyoxal, dimethylglyoxal, and propenylglyoxal are compared for several different conformations of the constituent molecules. The enols were found to be poorer electron acceptors than their respective keto isomers.
Molecular orbital theory of the properties of inorganic and organometallic compounds 4. Extended basis sets for third‐and fourth‐row, main‐group elements
Authors: Dobbs K. D. , Hehre W. J.
Published: January 2005

Two new series of efficient basis sets for third‐ and fourth‐row, main‐group elements have been developed. Split‐valence 3‐21G basis sets have been formulated from the minimal expansions by Huzinaga, in which each atomic orbital has been represented by a sum of three Gaussians. The original expansions for s− and p−type orbitals (except those for 1s) have been replaced by new combinations in which the two sets of orbitals (of the same n quantum number) share Gaussian exponents. The Huzinaga expansions for 1s, 3d and 4d (fourth‐row elements only) have been employed without further alteration. The valence atomic functions 4s, 4p for third‐row elements; 5s, 5p for fourth‐row elements have been split into two and one Gaussian parts. Supplemented 3‐21G(*) representations have been formed from the 3‐21G basis sets by the addition of a set of single d−type Gaussian functions.

The performance of 3‐21G and 3‐21G(*) basis sets is examined with regard to the calculation of equilibrium geometries, normal mode vibrational frequencies, reaction energies, and electric dipole moments involving a variety of normal and hypervalent compounds containing third‐ and fourth‐row, main‐group elements. The supplementary functions incorporated into the 3‐21G(*) basis sets are generally found to be important, especially for the proper description of equilibrium bond lengths and electric dipole moments. 3‐21G(*) representations are recommended for general use in lieu of the unsupplemented 3‐21G basis sets.
An SCF and CI Study of the 1,3 Shift in the HXCHY⇌XCHYH Isoelectronic Series: X, YCH2, NH, and O
Authors: Poirier Raymond A. , Majlessi Dariush , Zielinski Theresa J.
Published: January 2005

Ab initio molecular orbital calculations at SCF level with the 3‐21G, 6‐31G, and 6‐31G** basis sets and CI level with the 6‐31G basis set have been carried out for an isoelectronic series HXCHY and XCHYH, where X, Y can be CH2, NH, and O. Optimized structures (3‐21G and 6‐31G**) for both tautomers and the 1,3 hydrogen shift transition states are reported. The relative stabilities of the isomers and the barriers of the 1,3 shift are discussed in terms of proton affinities and bond orders. It is shown that both the relative stabilities of the tautomers and the relative barrier heights can be explained qualitatively using simple proton affinity arguments and that the barrier heights are quantitatively related to bond orders.
Optimization of the Generalized Valence Bond Method for Vector Processors
Authors: Bair Raymond A.
Published: January 2005

The Generalized Valence Bond [GVB(pp)] multiconfiguration self‐consistent field wave function optimization program has undergone substantial revision in migration from serial scalar computers (like IBM and VAX) to the FPS‐164, a minisupercomputer. Many of the code optimization strategies applied to the GVB program are portable and applicable to a wide range of scientific application codes. In benchmark calculations, the optimized FPS‐164 program, GVB164, is 6.5 times faster than the initial FPS‐164 implementation, both programs storing the two‐electron integral list on disk. GVB164 runs 30 times faster in wall time (limited by the FPS‐164 disk access speed) than a reference version of GVB2P5 on the VAX 11/780. The performance of GVB164 nearly doubles again when all of the two‐electron integrals can be stored in main memory.
Atomic Charges in the Quadrupole Solvation Energy Calculations
Authors: Dos̆en‐Mićović Ljiljana
Published: January 2005

A procedure is described and tested for the use of atomic charges instead of bond dipole moments in the calculations, based on the reaction field theory, of quadrupole term of the solvation energy.
A Strategy for the Regional Characterization of Potential Energy Surfaces
Authors: Yeh You‐Hsing , Fink William H.
Published: January 2005

The problem of characterization of a region of an n‐dimensional potential energy surface with maximization of the quality of representation for a given amount of computational effort is examined with the aid of well known theorems from numerical analysis. A choice of nonlinear grid and a representation of the potential expanded in Chebyshev polynomials is shown to be efficient. The strategy was applied to a two‐dimensional analytical representation of a transition state and to the ground‐state equilibrium geometry region of the Hartree‐Fock potential energy surface obtained with split‐valence basis sets for H2O, H2S, and H2Se. Results are reported for the equilibrium geometries and force constants for these molecules. Results are comparable to those obtained by others for H2O and H2S. A full set of values is reported for H2Se.
On the Enumeration of 2‐Factors of Polyhexes
Authors: Knop J. V. , Müller W. R. , Szymanski K. , Trinajstić N.
Published: January 2005

An algorithm is developed for enumerating all 2‐factors of polyhexes. Some properties of 2‐factors of polyhexes are discussed.
Offcenter Molecular Charge Distribution Corrections to Born Equation Electrostatic Solvation Energies
Authors: Ehrenson S.
Published: January 2005

Use of simple model charge distributions and classical multipolar dielectric theory has allowed investigation of the corrections appropriate to the Born equation for structured ion solutes. Among the results obtained for centrosymmetric charge distributions, but presumably of general consequence, are the demonstration of nonlinear dependence and great sensitivity of polarization to charge‐cavity boundary proximity, rapid falloff of effects upon continued subdivision of charge, and the significance of solvation energy differences for 2‐ and 3‐dimensional charge distributions. That 50% or greater corrections to the Born energy may readily be obtained in real ion systems, and the lack of sensitivity of such corrections to the dielectric of the medium for ε > 10 are also results of general interest. Analytical approximations for the electrostatic work equations appropriate to high dielectric solvation are included, and how uncertainties in charge magnitude and position for real ions might affect the analysis are also briefly considered.
On calculations of intermolecular potentials
Authors: Bhanuprakash K. , Kulkarni G. V. , Chandra Asish K.
Published: January 2005

Ab initio MO calculations of intermolecular potentials using conventional Gaussian basis set have a tendency to over emphasize binding due to underestimation of exchange repulsion. A modified semi‐empirical method has been suggested and results are found to be reliable at medium‐ and long‐range separation.
Recursion formulae for calculation of overlap integrals
Authors: Datta N. C. , Sen B.
Published: January 2005

Multi‐ζ Slater‐type orbitals are frequently used in molecular orbital calculations. Master formulae and numerical tables are available in literature for overlap integrals between s, p, and d atomic orbitals up to principal quantum number (n) = 3 and for some other selected quantum numbers. However, no master formula or numerical table is available for quantum numbers n = 5 and above and involving ƒ orbitals. In this article recursion formulae have been presented for the calculation of the overlap integral between any two s, p, d, and ƒ atomic orbitals formed by a linear combination of Slater‐type orbitals. These formulae, when expanded, would give rise to all the master formulae reported in the literature as well as formulae hitherto unreported.
Recent advances in multireference second order perturbation CI: The CIPSI method revisited
Authors: Cimiraglia Renzo , Persico Maurizio
Published: January 2005

The evolution of the CIPSI method, with the latest modifications recently implemented in our laboratory, is described. A new version, based on a diagrammatic technique, is presented. Test calculations which have been run on water, ethylene, and transacrolein, show that the new method is a powerful tool for the study of medium‐size molecular systems.
Character tables and symmetry eigenvectors for two C3v rotor molecular systems
Authors: Smeyers Yves G. , Niño A.
Published: January 2005

The character tables of the Altmann groups for the double internal rotation of C3v rotor molecules of different symmetries were determined. These symmetries were those of para‐xylene, trans‐1,2‐dimethylcyclopropane, cis‐N‐methylethylidenimine, dimethylamine, and a dimethylated asymmetrical molecule. From these character tables, the symmetry eigenvectors, which block diagonalize the Hamiltonian matrix, were deduced. The symmetry eigenvectors were derived with the help of a small computer.
Computer enumeration and generation of physical trees
Authors: Knop J. V. , Müller W. R. , Szymanski K. , Kroto H. W. , Trinajstić N.
Published: January 2005

A computer‐oriented method for the enumeration and generation of physical trees is presented. Physical trees depict acyclic chemical structures, but the term physical is used to stress the process by which the structures are produced.
CNDO Force constants for glucose
Authors: Back D. M. , Polavarapu P. L.
Published: January 2005

Force constants for both anomers of glucose are evaluated using CNDO/Force method.
A study of basis set effects on structures and electronic structures of phosphine oxide and fluorophosphine oxide
Authors: Streitwieser Andrew , McDowell Robert S. , Glaser Rainer
Published: January 2005

A variety of basis sets have been used for geometric and electronic structure studies. Electronic effects were measured using integrated spatial electron populations (ISEP). The two largest basis sets used, 6‐31G* and DZ+P, give significantly different results. Use of two d‐orbital sets (6‐31G*[dd]) or decontraction of the 2sp shell on phosphorus has little further effect. d‐Orbitals on oxygen are required for consistent electronic structure results, and d‐orbitals on fluorine have a small but significant effect. Use of diffuse functions, required for anions, is not recommended with small basis sets on neutral molecules. Large negative charges (≈−1.5) on oxygen are given by all of the larger basis sets by the ISEP procedure and indicate that the PO bond in these compounds is largely semi‐polar. The best simple symbolic representation of phosphine oxide is H3P+0−, rather than H3P0.
Basis set and correlation effects on computed positive ion hydrogen bond energies of the complexes AHn · AHn + 1+1: AHn = NH3, OH2, and FH
Authors: Del Bene Janet E.
Published: January 2005

Basis set expansion and correlation effects on computed hydrogen bond energies of the positive ion complexes AHn · AHn + 1+1, for AHn = NH3, OH2 and FH, have been evaluated. The addition of diffuse functions on nonhydrogen atoms is the single most important enhancement of split‐valence plus polarization basis sets for computing hydrogen bond energies. Basis set enhancement effects appear to be additive in these systems. The correlation energy contribution to the stabilization energies of these complexes is significant, with the second order term being the largest term and having a stabilizing effect. The third order term is smaller and of opposite sign, while the fourth order term is smaller yet and stabilizing. As a result, computed MP4 stabilization energies are bracketed by the MP2 and MP3 energies. The overall effect of basis set enhancement is to decrease hydrogen bond energies, whereas the addition of electron correlation increases stabilization energies.
Revised algorithms for the build‐up procedure for predicting protein conformations by energy minimization
Authors: Gibson K. D. , Scheraga H. A.
Published: January 2005

The build‐up procedure for predicting low‐energy conformations of polypeptides has been extended to cover the case of peptides in aqueous solutions. The revised procedure consists of five steps to be applied to each stage of the build‐up. I. All low‐energy minima of each of the two fragments to be joined are combined as starting points for energy minimization of the enlarged fragment, and those minima of the enlarged fragment within a certain upper bound of the lowest energy are retained. II. Whenever one of the combinations in Step I leads to an atomic overlap, the minimization is started again using a pseudoenergy function which remains finite everywhere and becomes equal to the standard energy function when no atoms overlap. III. The minima generated in Steps I and II are culled by ignoring side‐chain conformations and retaining only those minima whose backbone conformations differ significantly. IV. The rotameric states of the side chains are optimized, by testing their energy of interaction with the rest of the molecule, and subjecting the whole molecule to a further round of energy minimization if the test indicates that this would reduce the energy. V. The energies of all minima are recomputed with inclusion of a term for solvation and with a smaller upper bound as the criterion for retention. The original build‐up procedure consisted of Steps I and III only. Examples are presented showing the effectiveness of the new Steps II and IV in locating low‐energy minima, and the problems that remain to be solved, chiefly concerning Step V, are discussed.
Atomic charges derived from electrostatic potentials: A detailed study
Authors: Chirlian Lisa Emily , Francl Michelle Miller
Published: January 2005

A new algorithm for fitting atomic charges to molecular electrostatic potentials is presented. This method is non‐iterative and rapid compared to previous work. Results from a variety of gaussian basis sets, including STO‐3G, 3‐21G and 6‐31G*, are presented. Charges for a representative collection of molecules, comprising both first and second row atoms and anions are tabulated. The effects of using experimental and optimized geometries are explored. Charges derived from these fits are found to adequately reproduce SCF dipole moments. A small split valence representation, 3‐21G, appears to yield consistently good results in a reasonable amount of time.
Computer enumeration of polyhexes using the compact naming approach
Authors: Cioslowski J.
Published: January 2005

The enumeration of polyhexes can be easily carried out by utilizing a compact name (CN) approach to code chemical structures. The Fortran program performing generation of benzenoid hydrocarbons with 1–10 rings is presented. The computed structures are divided into various classes according to their cata‐ or peri‐ as well and non‐ or radicaloid character. Use of the additive nodal increments (ANI) approach leads to algorithm producing representative samples of the polyhexes' sets which can be applicable in testing of various topological formulae.
On color polynomials of Fibonacci graphs
Authors: El‐Basil Sherif
Published: January 2005

A recursion exists among the coefficients of the color polynomials of some of the families of graphs considered in recent work of Balasubramanian and Ramaraj. Such families of graphs have been called Fibonacci graphs. Application to king patterns of lattices is given. The method described here applies only to the so called Fibonacci graphs.
A note on the efficient and accurate computation of the phase functions ϕ and χ in semiclassical approximations
Authors: Senn Peter
Published: January 2005

Efficient and accurate algorithms for the computation of two so‐called phase functions which arise in semiclassical approximations are presented together with results from checks on their accuracy.
An efficient newton‐like method for molecular mechanics energy minimization of large molecules
Authors: Ponder Jay W. , Richards Frederic M.
Published: January 2005

Techniques from numerical analysis and crystallographic refinement have been combined to produce a variant of the Truncated Newton nonlinear optimization procedure. The new algorithm shows particular promise for potential energy minimization of large molecular systems. Usual implementations of Newton's method require storage space proportional to the number of atoms squared (i.e., O(N2)) and computer time of O(N3). Our suggested implementation of the Truncated Newton technique requires storage of less than O(N1.5) and CPU time of less than O(N2) for structures containing several hundred to a few thousand atoms. The algorithm exhibits quadratic convergence near the minimum and is also very tolerant of poor initial structures. A comparison with existing optimization procedures is detailed for cyclohexane, arachidonic acid, and the small protein crambin. In particular, a structure for crambin (662 atoms) has been refined to an RMS gradient of 3.6 × 10−6 kcal/mol/Å per atom on the MM2 potential energy surface. Several suggestions are made which may lead to further improvement of the new method.
A powerful truncated Newton method for potential energy minimization
Authors: Schlick Tamar , Overton Michael
Published: January 2005

With advances in computer architecture and software, Newton methods are becoming not only feasible for large‐scale nonlinear optimization problems, but also reliable, fast and efficient. Truncated Newton methods, in particular, are emerging as a versatile subclass. In this article we present a truncated Newton algorithm specifically developed for potential energy minimization. The method is globally convergent with local quadratic convergence. Its key ingredients are: (1) approximation of the Newton direction far away from local minima, (2) solution of the Newton equation iteratively by the linear Conjugate Gradient method, and (3) preconditioning of the Newton equation by the analytic second‐derivative components of the “local” chemical interactions: bond length, bond angle and torsional potentials. Relaxation of the required accuracy of the Newton search direction diverts the minimization search away from regions where the function is nonconvex and towards physically interesting regions. The preconditioning strategy significantly accelerates the iterative solution for the Newton search direction, and therefore reduces the computation time for each iteration. With algorithmic variations, the truncated Newton method can be formulated so that storage and computational requirements are comparable to those of the nonlinear Conjugate Gradient method. As the convergence rate of nonlinear Conjugate Gradient methods is linear and performance less predictable, the application of the truncated Newton code to potential energy functions is promising.
Refined ab initio 6‐31G split‐valence basis set optimization of the molecular structures of biphenyl in twisted, planar, and perpendicular conformations
Authors: Häfelinger Günter , Regelmann Claus
Published: January 2005

Improved full ab initio optimizations of the molecular structure of biphenyl in twisted minimum energy, coplanar, and perpendicular conformations by use of Poles's GAUSSIAN 82 program have been performed in the 6‐31G basis set. These lead to geometries and energies of much higher reliability than our earlier STO‐3G results. The torsional angle Φmin obtained now is 45.41° in close agreement with the recent experimental value of 44.4° ± 1.2°. Calculated CC distances may be converted to experimental ED rg‐values by means of independently determined linear regression correlations with very high statistical confidence, although they agree better with experimental x ray data for coplanar biphenyl without this correction. Calculated intramolecular angles are very similar for both STO‐3G and 6‐31G basis sets. The calculated torsional energy barrier towards Φ = 90° (ΔE90) is 6.76 kJ/mol in close agreement with the experimental‐31G value of 6.5 ± 2.0 kJ/mol. For coplanar biphenyl with D2h‐symmetry the calculated torsional energy barrier ΔE0 is 13.26 kJ/mol which is surprisingly much higher than the experimental value of 6.0 ± 2.1 kJ/mol. This discrepancy could not be resolved by optimizations assumed for two kinds of distortions of planarity of orthohydrogens from the molecular plane of the coplanar carbon atoms. But for the twisted minimum energy conformation asymmetric bending of ortho‐H atoms lead to a torsional angle Φmin = 44.74° together with a dihedral angle towards ortho‐H of 1.22°, and consequently even to an increase of torsional energy barriers to ΔE0 = 13.51 and ΔE90 = 6.91 kJ/mol.
A force field for allenes and for nonlinear acetylenes within the MM2 approximation
Authors: Allinger Norman L. , Pathiaseril Ahammadunny
Published: January 2005

Geometries and heats of formation for allenes may now be calculated with an extended version of MM2. The torsional barriers about bonds in an acetylenic unit are much more complicated than originally thought, if the unit is nonlinear. Ab initio calculations have been used to show just what these torsional barriers are, and the MM2 force field has been adapted to this information.