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Friday, August 26, 2022

Microcode

From Wikipedia, the free encyclopedia

In processor design, microcode (μcode) is a technique that interposes a layer of computer organization between the central processing unit (CPU) hardware and the programmer-visible instruction set architecture of a computer. Microcode is a layer of hardware-level instructions that implement higher-level machine code instructions or internal finite-state machine sequencing in many digital processing elements. Microcode is used in general-purpose central processing units, although in current desktop CPUs, it is only a fallback path for cases that the faster hardwired control unit cannot handle.

Microcode typically resides in special high-speed memory and translates machine instructions, state machine data, or other input into sequences of detailed circuit-level operations. It separates the machine instructions from the underlying electronics so that instructions can be designed and altered more freely. It also facilitates the building of complex multi-step instructions, while reducing the complexity of computer circuits. Writing microcode is often called microprogramming and the microcode in a particular processor implementation is sometimes called a microprogram.

More extensive microcoding allows small and simple microarchitectures to emulate more powerful architectures with wider word length, more execution units and so on, which is a relatively simple way to achieve software compatibility between different products in a processor family.

Some hardware vendors, especially IBM, use the term microcode as a synonym for firmware. In that way, all code within a device is termed microcode regardless of it being microcode or machine code; for example, hard disk drives are said to have their microcode updated, though they typically contain both microcode and firmware.

Overview

The lowest layer in a computer's software stack is traditionally raw machine code instructions for the processor. In microcoded processors, fetching and decoding those instructions. and executing them, may be done by microcode. To avoid confusion, each microprogram-related element is differentiated by the micro prefix: microinstruction, microassembler, microprogrammer, microarchitecture, etc.

Complex digital processors may also employ more than one (possibly microcode-based) control unit in order to delegate sub-tasks that must be performed essentially asynchronously in parallel. For example, the VAX 9000 has a IBox unit to fetch and decode instructions, which it hands to a microcoded EBox unit to be executed, and the VAX 8800 has both a microcoded IBox and a microcoded EBox.

A high-level programmer, or even an assembly language programmer, does not normally see or change microcode. Unlike machine code, which often retains some backward compatibility among different processors in a family, microcode only runs on the exact electronic circuitry for which it is designed, as it constitutes an inherent part of the particular processor design itself.

Design

Engineers normally write the microcode during the design phase of a processor, storing it in a read-only memory (ROM) or programmable logic array (PLA) structure, or in a combination of both. However, machines also exist that have some or all microcode stored in static random-access memory (SRAM) or flash memory. This is traditionally denoted as writeable control store in the context of computers, which can be either read-only or read-write memory. In the latter case, the CPU initialization process loads microcode into the control store from another storage medium, with the possibility of altering the microcode to correct bugs in the instruction set, or to implement new machine instructions.

Microprograms

Microprograms consist of series of microinstructions, which control the CPU at a very fundamental level of hardware circuitry. For example, a single typical horizontal microinstruction might specify the following operations:

  • Connect register 1 to the A side of the ALU
  • Connect register 7 to the B side of the ALU
  • Set the ALU to perform two's-complement addition
  • Set the ALU's carry input to zero
  • Store the result value in register 8
  • Update the condition codes from the ALU status flags (negative, zero, overflow, and carry)
  • Microjump to a given microPC address for the next microinstruction

To simultaneously control all processor's features in one cycle, the microinstruction is often wider than 50 bits; e.g., 128 bits on a 360/85 with an emulator feature. Microprograms are carefully designed and optimized for the fastest possible execution, as a slow microprogram would result in a slow machine instruction and degraded performance for related application programs that use such instructions.

Justification

Microcode was originally developed as a simpler method of developing the control logic for a computer. Initially, CPU instruction sets were hardwired. Each step needed to fetch, decode, and execute the machine instructions (including any operand address calculations, reads, and writes) was controlled directly by combinational logic and rather minimal sequential state machine circuitry. While such hard-wired processors were very efficient, the need for powerful instruction sets with multi-step addressing and complex operations (see below) made them difficult to design and debug; highly encoded and varied-length instructions can contribute to this as well, especially when very irregular encodings are used.

Microcode simplified the job by allowing much of the processor's behaviour and programming model to be defined via microprogram routines rather than by dedicated circuitry. Even late in the design process, microcode could easily be changed, whereas hard-wired CPU designs were very cumbersome to change. Thus, this greatly facilitated CPU design.

From the 1940s to the late 1970s, a large portion of programming was done in assembly language; higher-level instructions mean greater programmer productivity, so an important advantage of microcode was the relative ease by which powerful machine instructions can be defined. The ultimate extension of this are "Directly Executable High Level Language" designs, in which each statement of a high-level language such as PL/I is entirely and directly executed by microcode, without compilation. The IBM Future Systems project and Data General Fountainhead Processor are examples of this. During the 1970s, CPU speeds grew more quickly than memory speeds and numerous techniques such as memory block transfer, memory pre-fetch and multi-level caches were used to alleviate this. High-level machine instructions, made possible by microcode, helped further, as fewer more complex machine instructions require less memory bandwidth. For example, an operation on a character string can be done as a single machine instruction, thus avoiding multiple instruction fetches.

Architectures with instruction sets implemented by complex microprograms included the IBM System/360 and Digital Equipment Corporation VAX. The approach of increasingly complex microcode-implemented instruction sets was later called complex instruction set computer (CISC). An alternate approach, used in many microprocessors, is to use one or more programmable logic array (PLA) or read-only memory (ROM) (instead of combinational logic) mainly for instruction decoding, and let a simple state machine (without much, or any, microcode) do most of the sequencing. The MOS Technology 6502 is an example of a microprocessor using a PLA for instruction decode and sequencing. The PLA is visible in photomicrographs of the chip, and its operation can be seen in the transistor-level simulation.

Microprogramming is still used in modern CPU designs. In some cases, after the microcode is debugged in simulation, logic functions are substituted for the control store. Logic functions are often faster and less expensive than the equivalent microprogram memory.

Benefits

A processor's microprograms operate on a more primitive, totally different, and much more hardware-oriented architecture than the assembly instructions visible to normal programmers. In coordination with the hardware, the microcode implements the programmer-visible architecture. The underlying hardware need not have a fixed relationship to the visible architecture. This makes it easier to implement a given instruction set architecture on a wide variety of underlying hardware micro-architectures.

The IBM System/360 has a 32-bit architecture with 16 general-purpose registers, but most of the System/360 implementations use hardware that implements a much simpler underlying microarchitecture; for example, the System/360 Model 30 has 8-bit data paths to the arithmetic logic unit (ALU) and main memory and implemented the general-purpose registers in a special unit of higher-speed core memory, and the System/360 Model 40 has 8-bit data paths to the ALU and 16-bit data paths to main memory and also implemented the general-purpose registers in a special unit of higher-speed core memory. The Model 50 has full 32-bit data paths and implements the general-purpose registers in a special unit of higher-speed core memory. The Model 65 through the Model 195 have larger data paths and implement the general-purpose registers in faster transistor circuits. In this way, microprogramming enabled IBM to design many System/360 models with substantially different hardware and spanning a wide range of cost and performance, while making them all architecturally compatible. This dramatically reduces the number of unique system software programs that must be written for each model.

A similar approach was used by Digital Equipment Corporation (DEC) in their VAX family of computers. As a result, different VAX processors use different microarchitectures, yet the programmer-visible architecture does not change.

Microprogramming also reduces the cost of field changes to correct defects (bugs) in the processor; a bug can often be fixed by replacing a portion of the microprogram rather than by changes being made to hardware logic and wiring.

History

In 1947, the design of the MIT Whirlwind introduced the concept of a control store as a way to simplify computer design and move beyond ad hoc methods. The control store is a diode matrix: a two-dimensional lattice, where one dimension accepts "control time pulses" from the CPU's internal clock, and the other connects to control signals on gates and other circuits. A "pulse distributor" takes the pulses generated by the CPU clock and breaks them up into eight separate time pulses, each of which activates a different row of the lattice. When the row is activated, it activates the control signals connected to it.

Described another way, the signals transmitted by the control store are being played much like a player piano roll. That is, they are controlled by a sequence of very wide words constructed of bits, and they are played sequentially. In a control store, however, the song is short and repeated continuously.

In 1951, Maurice Wilkes enhanced this concept by adding conditional execution, a concept akin to a conditional in computer software. His initial implementation consisted of a pair of matrices: the first one generated signals in the manner of the Whirlwind control store, while the second matrix selected which row of signals (the microprogram instruction word, so to speak) to invoke on the next cycle. Conditionals were implemented by providing a way that a single line in the control store could choose from alternatives in the second matrix. This made the control signals conditional on the detected internal signal. Wilkes coined the term microprogramming to describe this feature and distinguish it from a simple control store.

Examples

  • The EMIDEC 1100 reputedly uses a hard-wired control store consisting of wires threaded through ferrite cores, known as "the laces".
  • Most models of the IBM System/360 series are microprogrammed:
    • The Model 25 is unique among System/360 models in using the top 16 K bytes of core storage to hold the control storage for the microprogram. The 2025 uses a 16-bit microarchitecture with seven control words (or microinstructions). After system maintenance or when changing operating mode, the microcode is loaded from the card reader, tape, or other device. The IBM 1410 emulation for this model is loaded this way.
    • The Model 30 uses an 8-bit microarchitecture with only a few hardware registers; everything that the programmer saw is emulated by the microprogram. The microcode for this model is also held on special punched cards, which are stored inside the machine in a dedicated reader per card, called "CROS" units (Capacitor Read-Only Storage). Another CROS unit is added for machines ordered with 1401/1440/1460 emulation and for machines ordered with 1620 emulation.
    • The Model 40 uses 56-bit control words. The 2040 box implements both the System/360 main processor and the multiplex channel (the I/O processor). This model uses TROS dedicated readers similar to CROS units, but with an inductive pickup (Transformer Read-only Store).
    • The Model 50 has two internal datapaths which operated in parallel: a 32-bit datapath used for arithmetic operations, and an 8-bit data path used in some logical operations. The control store uses 90-bit microinstructions.
    • The Model 85 has separate instruction fetch (I-unit) and execution (E-unit) to provide high performance. The I-unit is hardware controlled. The E-unit is microprogrammed; the control words are 108 bits wide on a basic 360/85 and wider if an emulator feature is installed.
  • The NCR 315 is microprogrammed with hand wired ferrite cores (a ROM) pulsed by a sequencer with conditional execution. Wires routed through the cores are enabled for various data and logic elements in the processor.
  • The Digital Equipment Corporation PDP-11 processors, with the exception of the PDP-11/20, are microprogrammed.
  • Most Data General Eclipse minicomputers are microprogrammed. The task of writing microcode for the Eclipse MV/8000 is detailed in the Pulitzer Prize-winning book titled The Soul of a New Machine.
  • Many systems from Burroughs are microprogrammed:
  • The B700 "microprocessor" execute application-level opcodes using sequences of 16-bit microinstructions stored in main memory; each of these is either a register-load operation or mapped to a single 56-bit "nanocode" instruction stored in read-only memory. This allows comparatively simple hardware to act either as a mainframe peripheral controller or to be packaged as a standalone computer.
  • The B1700 is implemented with radically different hardware including bit-addressable main memory but has a similar multi-layer organisation. The operating system preloads the interpreter for whatever language is required. These interpreters present different virtual machines for COBOL, Fortran, etc.
  • The VU0 and VU1 vector units in the Sony PlayStation 2 are microprogrammable; in fact, VU1 is only accessible via microcode for the first several generations of the SDK.
  • The MicroCore Labs MCL86 , MCL51 and MCL65 are examples of highly encoded "vertical" microsequencer implementations of the Intel 8086/8088, 8051, and MOS 6502.
  • The Digital Scientific Corp. Meta 4 Series 16 computer system was a user-microprogammable system first available in 1970. The microcode had a primarily vertical style with 32-bit microinstructions. The instructions were stored on replaceable program boards with a grid of bit positions. One (1) bits were represented by small metal squares that were sensed by amplifiers, zero (0) bits by the absence of the squares. The system could be configured with up to 4K 16-bit words of microstore. One of Digital Scientific's products was an emulator for the IBM 1130.
  • The MCP-1600 is a microprocessor made by Western Digital in the late 1970s through the early 1980s used to implement three different computer architectures in microcode: the Pascal MicroEngine, the WD16, and the DEC LSI-11, a cost-reduced PDP-11.
  • Earlier x86 processors are fully microcoded; starting with the Intel 80486, less complicated instructions are implemented directly in hardware. x86 processors implemented patchable microcode (patch by BIOS or operating system) since Intel P6 microarchitecture and AMD K7 microarchitecture.
  • Some video cards, wireless network interface controllers implemented patchable microcode (patch by operating system).

Implementation

Each microinstruction in a microprogram provides the bits that control the functional elements that internally compose a CPU. The advantage over a hard-wired CPU is that internal CPU control becomes a specialized form of a computer program. Microcode thus transforms a complex electronic design challenge (the control of a CPU) into a less complex programming challenge. To take advantage of this, a CPU is divided into several parts:

  • An I-unit may decode instructions in hardware and determine the microcode address for processing the instruction in parallel with the E-unit.
  • A microsequencer picks the next word of the control store. A sequencer is mostly a counter, but usually also has some way to jump to a different part of the control store depending on some data, usually data from the instruction register and always some part of the control store. The simplest sequencer is just a register loaded from a few bits of the control store.
  • A register set is a fast memory containing the data of the central processing unit. It may include the program counter and stack pointer, and may also include other registers that are not easily accessible to the application programmer. Often the register set is a triple-ported register file; that is, two registers can be read, and a third written at the same time.
  • An arithmetic and logic unit performs calculations, usually addition, logical negation, a right shift, and logical AND. It often performs other functions, as well.

There may also be a memory address register and a memory data register, used to access the main computer storage. Together, these elements form an "execution unit". Most modern CPUs have several execution units. Even simple computers usually have one unit to read and write memory, and another to execute user code. These elements could often be brought together as a single chip. This chip comes in a fixed width that would form a "slice" through the execution unit. These are known as "bit slice" chips. The AMD Am2900 family is one of the best known examples of bit slice elements. The parts of the execution units and the whole execution units are interconnected by a bundle of wires called a bus.

Programmers develop microprograms, using basic software tools. A microassembler allows a programmer to define the table of bits symbolically. Because of its close relationship to the underlying architecture, "microcode has several properties that make it difficult to generate using a compiler." A simulator program is intended to execute the bits in the same way as the electronics, and allows much more freedom to debug the microprogram. After the microprogram is finalized, and extensively tested, it is sometimes used as the input to a computer program that constructs logic to produce the same data. This program is similar to those used to optimize a programmable logic array. Even without fully optimal logic, heuristically optimized logic can vastly reduce the number of transistors from the number needed for a read-only memory (ROM) control store. This reduces the cost to produce, and the electricity used by, a CPU.

Microcode can be characterized as horizontal or vertical, referring primarily to whether each microinstruction controls CPU elements with little or no decoding (horizontal microcode) or requires extensive decoding by combinatorial logic before doing so (vertical microcode). Consequently, each horizontal microinstruction is wider (contains more bits) and occupies more storage space than a vertical microinstruction.

Horizontal microcode

"Horizontal microcode has several discrete micro-operations that are combined in a single microinstruction for simultaneous operation." Horizontal microcode is typically contained in a fairly wide control store; it is not uncommon for each word to be 108 bits or more. On each tick of a sequencer clock a microcode word is read, decoded, and used to control the functional elements that make up the CPU.

In a typical implementation a horizontal microprogram word comprises fairly tightly defined groups of bits. For example, one simple arrangement might be:

Register source A Register source B Destination register Arithmetic and logic unit operation Type of jump Jump address

For this type of micromachine to implement a JUMP instruction with the address following the opcode, the microcode might require two clock ticks. The engineer designing it would write microassembler source code looking something like this:

  # Any line starting with a number-sign is a comment
  # This is just a label, the ordinary way assemblers symbolically represent a 
  # memory address.
InstructionJUMP:
      # To prepare for the next instruction, the instruction-decode microcode has already
      # moved the program counter to the memory address register. This instruction fetches
      # the target address of the jump instruction from the memory word following the
      # jump opcode, by copying from the memory data register to the memory address register.
      # This gives the memory system two clock ticks to fetch the next 
      # instruction to the memory data register for use by the instruction decode.
      # The sequencer instruction "next" means just add 1 to the control word address.
   MDR, NONE, MAR, COPY, NEXT, NONE
      # This places the address of the next instruction into the PC.
      # This gives the memory system a clock tick to finish the fetch started on the
      # previous microinstruction.
      # The sequencer instruction is to jump to the start of the instruction decode.
   MAR, 1, PC, ADD, JMP, InstructionDecode
      # The instruction decode is not shown, because it is usually a mess, very particular
      # to the exact processor being emulated. Even this example is simplified.
      # Many CPUs have several ways to calculate the address, rather than just fetching
      # it from the word following the op-code. Therefore, rather than just one
      # jump instruction, those CPUs have a family of related jump instructions.

For each tick it is common to find that only some portions of the CPU are used, with the remaining groups of bits in the microinstruction being no-ops. With careful design of hardware and microcode, this property can be exploited to parallelise operations that use different areas of the CPU; for example, in the case above, the ALU is not required during the first tick, so it could potentially be used to complete an earlier arithmetic instruction.

Vertical microcode

In vertical microcode, each microinstruction is significantly encoded, that is, the bit fields generally pass through intermediate combinatory logic that, in turn, generates the control and sequencing signals for internal CPU elements (ALU, registers, etc.). This is in contrast with horizontal microcode, in which the bit fields either directly produce the control and sequencing signals or are only minimally encoded. Consequently, vertical microcode requires smaller instruction lengths and less storage, but requires more time to decode, resulting in a slower CPU clock.

Some vertical microcode is just the assembly language of a simple conventional computer that is emulating a more complex computer. Some processors, such as DEC Alpha processors and the CMOS microprocessors on later IBM mainframes System/390 and z/Architecture, use machine code, running in a special mode that gives it access to special instructions, special registers, and other hardware resources unavailable to regular machine code, to implement some instructions and other functions, such as page table walks on Alpha processors. This is called PALcode on Alpha processors and millicode on IBM mainframe processors.

Another form of vertical microcode has two fields:

Field select Field value

The field select selects which part of the CPU will be controlled by this word of the control store. The field value controls that part of the CPU. With this type of microcode, a designer explicitly chooses to make a slower CPU to save money by reducing the unused bits in the control store; however, the reduced complexity may increase the CPU's clock frequency, which lessens the effect of an increased number of cycles per instruction.

As transistors grew cheaper, horizontal microcode came to dominate the design of CPUs using microcode, with vertical microcode being used less often.

When both vertical and horizontal microcode are used, the horizontal microcode may be referred to as nanocode or picocode.

Writable control store

A few computers were built using writable microcode. In this design, rather than storing the microcode in ROM or hard-wired logic, the microcode is stored in a RAM called a writable control store or WCS. Such a computer is sometimes called a writable instruction set computer (WISC).

Many experimental prototype computers use writable control stores; there are also commercial machines that use writable microcode, such as the Burroughs Small Systems, early Xerox workstations, the DEC VAX 8800 (Nautilus) family, the Symbolics L- and G-machines, a number of IBM System/360 and System/370 implementations, some DEC PDP-10 machines, and the Data General Eclipse MV/8000.

Many more machines offer user-programmable writable control stores as an option, including the HP 2100, DEC PDP-11/60 and Varian Data Machines V-70 series minicomputers. The IBM System/370 includes a facility called Initial-Microprogram Load (IML or IMPL) that can be invoked from the console, as part of power-on reset (POR) or from another processor in a tightly coupled multiprocessor complex.

Some commercial machines, for example IBM 360/85, have both a read-only storage and a writable control store for microcode.

WCS offers several advantages including the ease of patching the microprogram and, for certain hardware generations, faster access than ROMs can provide. User-programmable WCS allows the user to optimize the machine for specific purposes.

Starting with the Pentium Pro in 1995, several x86 CPUs have writable Intel Microcode. This, for example, has allowed bugs in the Intel Core 2 and Intel Xeon microcodes to be fixed by patching their microprograms, rather than requiring the entire chips to be replaced. A second prominent example is the set of microcode patches that Intel offered for some of their processor architectures of up to 10 years in age, in a bid to counter the security vulnerabilities discovered in their designs – Spectre and Meltdown – which went public at the start of 2018. A microcode update can be installed by Linux, FreeBSD, Microsoft Windows, or the motherboard BIOS.

Comparison to VLIW and RISC

The design trend toward heavily microcoded processors with complex instructions began in the early 1960s and continued until roughly the mid-1980s. At that point the RISC design philosophy started becoming more prominent.

A CPU that uses microcode generally takes several clock cycles to execute a single instruction, one clock cycle for each step in the microprogram for that instruction. Some CISC processors include instructions that can take a very long time to execute. Such variations interfere with both interrupt latency and, what is far more important in modern systems, pipelining.

When designing a new processor, a hardwired control RISC has the following advantages over microcoded CISC:

  • Programming has largely moved away from assembly level, so it's no longer worthwhile to provide complex instructions for productivity reasons.
  • Simpler instruction sets allow direct execution by hardware, avoiding the performance penalty of microcoded execution.
  • Analysis shows complex instructions are rarely used, hence the machine resources devoted to them are largely wasted.
  • The machine resources devoted to rarely used complex instructions are better used for expediting performance of simpler, commonly used instructions.
  • Complex microcoded instructions may require many clock cycles that vary, and are difficult to pipeline for increased performance.

There are counterpoints as well:

  • The complex instructions in heavily microcoded implementations may not take much extra machine resources, except for microcode space. For example, the same ALU is often used to calculate an effective address and to compute the result from the operands, e.g., the original Z80, 8086, and others.
  • The simpler non-RISC instructions (i.e., involving direct memory operands) are frequently used by modern compilers. Even immediate to stack (i.e., memory result) arithmetic operations are commonly employed. Although such memory operations, often with varying length encodings, are more difficult to pipeline, it is still fully feasible to do so - clearly exemplified by the i486, AMD K5, Cyrix 6x86, Motorola 68040, etc.
  • Non-RISC instructions inherently perform more work per instruction (on average), and are also normally highly encoded, so they enable smaller overall size of the same program, and thus better use of limited cache memories.

Many RISC and VLIW processors are designed to execute every instruction (as long as it is in the cache) in a single cycle. This is very similar to the way CPUs with microcode execute one microinstruction per cycle. VLIW processors have instructions that behave similarly to very wide horizontal microcode, although typically without such fine-grained control over the hardware as provided by microcode. RISC instructions are sometimes similar to the narrow vertical microcode.

Microcode has been popular in application-specific processors such as network processors, microcontrollers, digital signal processors, channel controllers, disk controllers, network interface controllers, graphics processing units, and in other hardware.

Micro-operations

Modern CISC implementations, such as the x86 family, decode instructions into dynamically buffered micro-operations ("μops") with an instruction encoding similar to RISC or traditional microcode. A hardwired instruction decode unit directly emits μops for common x86 instructions, but falls back to a more traditional microcode ROM containing μops for more complex or rarely used instructions.

For example, an x86 might look up μops from microcode to handle complex multistep operations such as loop or string instructions, floating-point unit transcendental functions or unusual values such as denormal numbers, and special-purpose instructions such as CPUID.

Emotion and memory

From Wikipedia, the free encyclopedia

Emotion can have a powerful effect on humans and animals. Numerous studies have shown that the most vivid autobiographical memories tend to be of emotional events, which are likely to be recalled more often and with more clarity and detail than neutral events.

The activity of emotionally enhanced memory retention can be linked to human evolution; during early development, responsive behavior to environmental events would have progressed as a process of trial and error. Survival depended on behavioral patterns that were repeated or reinforced through life and death situations. Through evolution, this process of learning became genetically embedded in humans and all animal species in what is known as flight or fight instinct.

Artificially inducing this instinct through traumatic physical or emotional stimuli essentially creates the same physiological condition that heightens memory retention by exciting neuro-chemical activity affecting areas of the brain responsible for encoding and recalling memory. This memory-enhancing effect of emotion has been demonstrated in many laboratory studies, using stimuli ranging from words to pictures to narrated slide shows, as well as autobiographical memory studies. However, as described below, emotion does not always enhance memory.

Arousal and valence in memory

One of the most common frameworks in the emotions field proposes that affective experiences are best characterized by two main dimensions: arousal and valence. The dimension of valence ranges from highly positive to highly negative, whereas the dimension of arousal ranges from calming or soothing to exciting or agitating.

The majority of studies to date have focused on the arousal dimension of emotion as the critical factor contributing to the emotional enhancement effect on memory. Different explanations have been offered for this effect, according to the different stages of memory formation and reconstruction.

However, a growing body of research is dedicated to the emotional valence dimension and its effects on memory. It has been claimed that this is an essential step towards a more complete understanding of emotion effects on memory. The studies that did investigate this dimension have found that emotional valence alone can enhance memory; that is, nonarousing items with positive or negative valence can be better remembered than neutral items.

Emotion and encoding

From an information processing perspective, encoding refers to the process of interpreting incoming stimuli and combining the processed information. At the encoding level the following mechanisms have been suggested as mediators of emotion effects on memory:

Selectivity of attention

Easterbrook's (1959) cue utilization theory predicted that high levels of arousal will lead to attention narrowing, defined as a decrease in the range of cues from the stimulus and its environment to which the organism is sensitive. According to this hypothesis, attention will be focused primarily on the arousing details (cues) of the stimulus, so that information central to the source of the emotional arousal will be encoded while peripheral details will not.

Accordingly, several studies have demonstrated that the presentation of emotionally arousing stimuli (compared to neutral stimuli) results in enhanced memory for central details (details central to the appearance or meaning of the emotional stimuli) and impaired memory for peripheral details. Also consistent with this hypothesis are findings of weapon focus effect, in which witnesses to a crime remember the gun or knife in great detail but not other details such as the perpetrator's clothing or vehicle. In laboratory replications it was found that participants spend a disproportionate amount of time looking at a weapon in a scene, and this looking time is inversely related to the likelihood that individuals will subsequently identify the perpetrator of the crime. Other researchers have suggested arousal may also increase the duration of attentional focusing on the arousing stimuli, thus delaying the disengagement of attention from it. Ochsner (2000) summarized the different findings and suggested that by influencing attention selectivity and dwell time, arousing stimuli are more distinctively encoded, resulting in more accurate memory of those stimuli.

While these previous studies focused on how emotion affects memory for emotionally arousing stimuli, in their arousal-biased competition theory, Mather and Sutherland (2011) argue that how arousal influences memory for non-emotional stimuli depends on the priority of those stimuli at the time of the arousal. Arousal enhances perception and memory of high priority stimuli but impairs perception and memory of low priority stimuli. Priority can be determined by bottom-up salience or by top-down goals.

Prioritized processing

Emotional items also appear more likely to be processed when attention is limited, suggesting a facilitated or prioritized processing of emotional information. This effect was demonstrated using the attentional blink paradigm in which 2 target items are presented in close temporal proximity within a stream of rapidly presented stimuli.

The typical finding is that participants often miss the second target item, as if there were a "blink" of attention following the first target's presentation, reducing the likelihood that the second target stimulus is attended. However, when the second target stimulus elicits emotional arousal (a "taboo" word), participants are less likely to miss the target's presentation, which suggests that under conditions of limited attention, arousing items are more likely to be processed than neutral items.

Additional support for the prioritized processing hypothesis was provided by studies investigating the visual extinction deficit. People suffering from this deficit can perceive a single stimulus in either side visual field if it is presented alone but are unaware of the same stimulus in the visual field opposed to the lesional side, if another stimulus is presented simultaneously on the lesional side.

Emotion has been found to modulate the magnitude of the visual extinction deficit, so that items that signal emotional relevance (e.g., spiders) are more likely to be processed in the presence of competing distractors than nonemotional items (e.g., flowers).

Emotion and storage

In addition to its effects during the encoding phase, emotional arousal appears to increase the likelihood of memory consolidation during the retention (storage) stage of memory (the process of creating a permanent record of the encoded information). A number of studies show that over time, memories for neutral stimuli decrease but memories for arousing stimuli remain the same or improve.

Others have discovered that memory enhancements for emotional information tend to be greater after longer delays than after relatively short ones. This delayed effect is consistent with the proposal that emotionally arousing memories are more likely to be converted into a relatively permanent trace, whereas memories for nonarousing events are more vulnerable to disruption.

A few studies have even found that emotionally arousing stimuli enhance memory only after a delay. The most famous of these was a study by Kleinsmith and Kaplan (1963) that found an advantage for numbers paired with arousing words over those paired with neutral words only at delayed test, but not at immediate test. As outlined by Mather (2007), the Kleinsmith and Kaplan effects were most likely due to a methodological confound. However, Sharot and Phelps (2004) found better recognition of arousing words over neutral words at a delayed test but not at an immediate test, supporting the notion that there is enhanced memory consolidation for arousing stimuli. According to these theories, different physiological systems, including those involved in the discharge of hormones believed to affect memory consolidation, become active during, and closely following, the occurrence of arousing events.

Another possible explanation for the findings of the emotional arousal delayed effect is post-event processing regarding the cause of the arousal. According to the post stimulus elaboration (PSE) hypothesis, an arousing emotional experience may cause more effort to be invested in elaboration of the experience, which would subsequently be processed at a deeper level than a neutral experience. Elaboration refers to the process of establishing links between newly encountered information and previously stored information.

It has long been known that when individuals process items in an elaborative fashion, such that meaning is extracted from items and inter-item associations are formed, memory is enhanced. Thus, if a person gives more thought to central details in an arousing event, memory for such information is likely to be enhanced. However, these processes could also disrupt consolidation of memories for peripheral details. Christianson (1992) suggested that the combined action of perceptual, attentional, and elaborative processing, triggered by an emotionally arousing experience, produces memory enhancements of details related to the emotion laden stimulus, at the cost of less elaboration and consolidation of memory for the peripheral details.

Emotion and elaboration

The processes involved in this enhancement may be distinct from those mediating the enhanced memory for arousing items. It has been suggested that in contrast to the relatively automatic attentional modulation of memory for arousing information, memory for non-arousing positive or negative stimuli may benefit instead from conscious encoding strategies, such as elaboration. This elaborative processing can be autobiographical or semantic.

Autobiographical elaboration is known to benefit memory by creating links between the processed stimuli, and the self, for example, deciding whether a word would describe the personal self. Memory formed through autobiographical elaboration is enhanced as compared to items processed for meaning, but not in relation to the self.

Since words such as "sorrow" or "comfort" may be more likely to be associated with autobiographical experiences or self-introspection than neutral words such as "shadow", autobiographical elaboration may explain the memory enhancement of non-arousing positive or negative items. Studies have shown that dividing attention at encoding decreases an individual's ability to utilize controlled encoding processes, such as autobiographical or semantic elaboration.

Thus, findings that participants' memory for negative non-arousing words suffers with divided attention, and that the memory advantage for negative, non-arousing words can be eliminated when participants encode items while simultaneously performing a secondary task, has supported the elaborative processing hypothesis as the mechanism responsible for memory enhancement for negative non-arousing words.

Emotion and retrieval

Retrieval is a process of reconstructing past experiences; this phenomenon of reconstruction is influenced by a number of different variables described below.

Trade-off between details

Kensinger argues there are two trade-offs: central/peripheral trade-off of details and a specific/general trade-off. Emotional memories may include increased emotional details often with the trade-off of excluding background information. Research has shown that this trade-off effect cannot be explained exclusively by overt attention (measured by eye-tracking directed to emotional items during encoding) (Steinmetz & Kensinger, 2013).

Contextual effects of emotion on memory

Contextual effects occur as a result of the degree of similarity between the encoding context and the retrieval context of an emotional dimension. The main findings are that the current mood we are in affects what is attended, encoded and ultimately retrieved, as reflected in two similar but subtly different effects: the mood congruence effect and mood-state dependent retrieval. Positive encoding contexts have been connected to activity in the right fusiform gyrus. Negative encoding contexts have been correlated to activity in the right amygdala (Lewis & Critchley, 2003). However, Lewis and Critchley (2003) claim that it is not clear whether involvement of the emotional system in encoding memory differs for positive or negative emotions, or whether moods at recall lead to activity in the corresponding positive or negative neural networks.

The mood congruence effect

The mood congruence effect refers to the tendency of individuals to retrieve information more easily when it has the same emotional content as their current emotional state. For instance, being in a depressed mood increases the tendency to remember negative events (Drace, 2013).

This effect has been demonstrated for explicit retrieval as well as implicit retrieval.

Mood-state dependent retrieval

Another documented phenomenon is the mood-state dependent retrieval, a type of context-dependent memory. The retrieval of information is more effective when the emotional state at the time of retrieval is similar to the emotional state at the time of encoding.

Thus, the probability of remembering an event can be enhanced by evoking the emotional state experienced during its initial processing. These two phenomena, the mood congruity effect, and mood-state dependent retrieval, are similar to the context effects which have been traditionally observed in memory research. It may also relate to the phenomena of state-dependent memory in neuropsychopharmacology.

When recalling a memory, if someone is recalling an event by themselves or within a group of people, the emotions that they remember may change as well recall of specific details. Individuals recall events with stronger negative emotions than when a group is recalling the same event. Collaborative recall, as it can be referred to, causes strong emotions to fade. Emotional tone changes as well, with a difference of individual or collaborative recall so much that an individual will keep the tone of what was previously felt, but the group will have a more neutral tone. For example, if someone is recalling the negative experience of taking a difficult exam, then they will talk in a negative tone. However, when the group is recalling taking the exam, they will most likely recount it in a positive tone as the negative emotions and tones fade. Detail recount is also something that changed based on the emotion state a person is in when they are remembering an event. If an event is being collaboratively recalled the specific detail count is higher than if an individual is doing it. Detail recall is also more accurate when someone is experiencing negative emotion; Xie and Zhang (2016) conducted a study in which participants saw a screen with five colors on it and when presented with the next screen were asked which color was missing. Those who were experiencing negative emotions were more precise than those in the positive and neutral conditions. Aside from emotional state, mental illness like depression relates to people's ability to recall specific details. Those who are depressed tend to overgeneralize their memories and are not able to remember as many specific details of any events as compared to those without depression.

Thematic vs. sudden appearance of emotional stimuli

A somewhat different contextual effect stemmed from the recently made distinction between thematical and sudden appearance of an emotionally arousing event, suggesting that the occurrence of memory impairments depends on the way the emotional stimuli are induced. Laney et al. (2003) argued that when arousal is induced thematically (i.e., not through the sudden appearance of a discrete shocking stimulus such as a weapon but rather through involvement in an unfolding event plot and empathy with the victim as his or her plight becomes increasingly apparent), memory enhancements of details central to the emotional stimulus need not come at the expense of memory impairment of peripheral details.

Laney et al. (2004) demonstrated this by using an audio narrative to give the presented slides either neutral or emotional meaning, instead of presenting shockingly salient visual stimuli. In one of the experiments, participants in both the neutral and emotional conditions viewed slides of a date scenario of a woman and man at a dinner date. The couple engaged in conversation, then, at the end of the evening, embraced. The event concluded with the man leaving and the woman phoning a friend.

The accompanying audio recording informed participants in the neutral condition that the date went reasonably well, while participants in the emotional condition heard that, as the evening wore on, the man displayed some increasingly unpleasant traits of a type that was derogatory to women, and the embrace at the end of the evening was described as an attempt to sexually assault the woman.

As expected, the results revealed that details central to the event were remembered more accurately when that event was emotional than when neutral, However, this was not at the expense of memory for peripheral (in this case, spatially peripheral or plot-irrelevant) details, which were also remembered more accurately when the event was emotional. Based on these findings it has been suggested that the dual enhancing and impairing effects on memory are not an inevitable consequence of emotional arousal.

Memory of felt emotion

Many researchers use self-report measures of felt emotion as a manipulation check. This raises an interesting question and a possible methodological weakness: are people always accurate when they recall how they felt in the past? Several findings suggest this is not the case. For instance, in a study of memory for emotions in supporters of former U.S. presidential candidate Ross Perot, supporters were asked to describe their initial emotional reactions after Perot's unexpected withdrawal in July 1992 and again after the presidential election that November.

Between the two assessment periods, the views of many supporters changed dramatically as Perot re-entered the race in October and received nearly a fifth of the popular vote. The results showed that supporters recalled their past emotions as having been more consistent with their current appraisals of Perot than they actually were.

Another study found that people's memories for how distressed they felt when they learned of the 9/11 terrorist attacks changed over time and moreover, were predicted by their current appraisals of the impact of the attacks (Levine et al., 2004). It appears that memories of past emotional responses are not always accurate, and can even be partially reconstructed based on their current appraisal of events.

Studies have shown that as episodic memory becomes less accessible over time, the reliance on semantic memory to remember past emotions increases. In one study Levine et al. (2009) primes of the cultural belief of women being more emotional than men had a greater effect on responses for older memories compared to new memories. The long-term recall of emotions was more in line with the primed opinions, showing that long-term recall of emotions was heavily influenced by current opinions.

Emotion regulation effects on memory

An interesting issue in the study of the emotion-memory relationship is whether our emotions are influenced by our behavioral reaction to them, and whether this reaction—in the form of expression or suppression of the emotion—might affect what we remember about an event. Researchers have begun to examine whether concealing feelings influences our ability to perform common cognitive tasks, such as forming memories, and found that the emotion regulation efforts do have cognitive consequences. In the seminal work on negative affect arousal and white noise, Seidner found support for the existence of a negative affect arousal mechanism through observations regarding the devaluation of speakers from other ethnic origins."

In a study of Richards and Gross (1999) and Tiwari (2013), participants viewed slides of injured men that produced increases in negative emotions, while information concerning each man was presented orally with his slide. The participants were assigned to either an expressive suppression group (where they were asked to refrain from showing emotion while watching the slides) or to a control group (where they were not given regulatory instructions at all). As predicted by the researchers, suppressors showed significantly worse performance on a memory test for the orally presented information.

In another study, it was investigated whether expressive suppression (i.e., keeping one's emotions subdued) comes with a cognitive price. They measured expressive suppression when it spontaneously occurred while watching a movie of surgeries. After the movie, memory was tested and was found to be worse with a higher usage of suppression. In a second study, another movie was shown of people arguing. Memory of the conversation was then measured. When gauging the magnitude of cognitive cost, expressive suppression was compared with self-distraction, which was described as simply not trying to think about something. It was concluded that experimentally-induced suppression was associated with worse memory.

There is evidence that emotion enhances memory but is more specific towards arousal and valence factors. To test this theory, arousal and valence were assessed for over 2,820 words. Both negative and positive stimuli were remembered higher than neutral stimuli. Arousal also did not predict recognition memory. In this study, the importance of stimulus controls and experimental designs in research memory was highlighted. Arousal-related activities when affiliated with heightened heart rate (HR) stimulate prediction of memory enhancement. It was hypothesized that tonic elevations in HR (meaning revitalization in HR) and phasic HR (meaning quick reaction) declaration to help the memory. Fifty-three men's heart rates were measured while looking at unpleasant, neutral, and pleasant pictures and their memory tested two days later. It was concluded that tonic elevations created more accurate memory recall.

Several related studies have reached similar results. It was demonstrated that the effects of expressive suppression on memory generalize to emotionally positive experiences and to socially relevant contexts.

One possible answer to the question "why does emotion suppression impair memory?" might lay in the self monitoring efforts invested in order to suppress emotion (thinking about the behavior one is trying to control). A recent study found heightened self- monitoring efforts among suppressors relative to control participants.

That is, suppressors were more likely to report thinking about their behavior and the need to control it during a conversation. Increases in self-monitoring predicted decreases in memory for what was said, that is, people who reported thinking a lot about controlling their behavior had particularly impoverished memories. However, additional research is needed to confirm whether self-monitoring actually exerts a causal effect on memory.

Emotion-induced forgetting

Emotionally arousing stimuli can lead to retrograde amnesia for preceding events and anterograde amnesia for subsequent events. This has been demonstrated in lab studies with lists of words or pictures, in which people show impaired memory for stimuli appearing before or after arousing stimuli.

Depression and memory

Memory recall tends to be congruent with one's current mood, with depressed people more likely to recall negative events from the past. In addition, depression is often associated with poor memory in general, as outlined here.

Dementia and emotional memory

Several studies have demonstrated emotional memory enhancement in Alzheimer's patients suggesting that emotional memory enhancement might be used in the daily management of Alzheimer's patients. One study found that objects are recalled significantly better in Alzheimer's patients if they were presented as birthday presents to AD patients.

Aging and emotional memory

The enhancing effects of emotional arousal on later memory recall tend to be maintained among older adults and the amygdala shows relatively less decline than many other brain regions. However, older adults also show somewhat of a shift towards favoring positive over negative information in memory, leading to a positivity effect.

Emotional memory and sleep

Emotional memory and sleep has been a well-researched association. Emotional memories are consolidated greater during sleep, rather than neutral memories. Studies have investigated high valence and arousing words, in comparison to neutral words. Sleep enhances the consolidation of the high valence and arousing words and therefore these are remembered more post-sleep. This concept has been demonstrated in many studies using a variety of media such as pictures, film clips, and words.

Memories of 'future relevance' are also consolidated greater during sleep. In a study by Wilhelm et al., 2011, memories of items that participants knew were needed for the future (for the testing session) were remembered more after sleep. Sleep consolidated these memories of future relevance to a greater extent. Memories that are emotionally significant and relevant for the future are therefore preferentially consolidated during sleep. This can translate to mean that memories that are more meaningful or valuable to a person are consolidated more.

The concept of emotional memory and sleep can be applied to real-life situations e.g. by developing more effective learning strategies. One could integrate the memorization of information that possesses high emotional significance (highly salient) with information that holds little emotional significance (low salience), prior to a period of sleep.

Molecule

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Molecule

Atomic force microscopy (AFM) image of a PTCDA molecule, in which the five six-carbon rings are visible.
 
A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings.
 
AFM image of 1,5,9-trioxo-13-azatriangulene and its chemical structure.

A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and molecule is often used when referring to polyatomic ions.

A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.g. water (two hydrogen atoms and one oxygen atom; H2O). In the kinetic theory of gases, the term molecule is often used for any gaseous particle regardless of its composition. This relaxes the requirement that a molecule contains two or more atoms, since the noble gases are individual atoms. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are typically not considered single molecules.

Concepts similar to molecules have been discussed since ancient times, but modern investigation into the nature of molecules and their bonds began in the 17th century. Refined over time by scientists such as Robert Boyle, Amedeo Avogadro, Jean Perrin, and Linus Pauling, the study of molecules is today known as molecular physics or molecular chemistry.

Etymology

According to Merriam-Webster and the Online Etymology Dictionary, the word "molecule" derives from the Latin "moles" or small unit of mass. The word is derived from French molécule (1678), from New Latin molecula, diminutive of Latin moles "mass, barrier". The word, which until the late 18th century was used only in Latin form, became popular after being used in works of philosophy by Descartes.

History

The definition of the molecule has evolved as knowledge of the structure of molecules has increased. Earlier definitions were less precise, defining molecules as the smallest particles of pure chemical substances that still retain their composition and chemical properties. This definition often breaks down since many substances in ordinary experience, such as rocks, salts, and metals, are composed of large crystalline networks of chemically bonded atoms or ions, but are not made of discrete molecules.

The modern concept of molecules can be traced back towards pre-scientific and Greek philosophers such as Leucippus and Democritus who argued that all the universe is composed of atoms and voids. Circa 450 BC Empedocles imagined fundamental elements (fire (Fire symbol (alchemical).svg), earth (Earth symbol (alchemical).svg), air (Air symbol (alchemical).svg), and water (Water symbol (alchemical).svg)) and "forces" of attraction and repulsion allowing the elements to interact.

A fifth element, the incorruptible quintessence aether, was considered to be the fundamental building block of the heavenly bodies. The viewpoint of Leucippus and Empedocles, along with the aether, was accepted by Aristotle and passed to medieval and renaissance Europe.

In a more concrete manner, however, the concept of aggregates or units of bonded atoms, i.e. "molecules", traces its origins to Robert Boyle's 1661 hypothesis, in his famous treatise The Sceptical Chymist, that matter is composed of clusters of particles and that chemical change results from the rearrangement of the clusters. Boyle argued that matter's basic elements consisted of various sorts and sizes of particles, called "corpuscles", which were capable of arranging themselves into groups. In 1789, William Higgins published views on what he called combinations of "ultimate" particles, which foreshadowed the concept of valency bonds. If, for example, according to Higgins, the force between the ultimate particle of oxygen and the ultimate particle of nitrogen were 6, then the strength of the force would be divided accordingly, and similarly for the other combinations of ultimate particles.

Amedeo Avogadro created the word "molecule". His 1811 paper "Essay on Determining the Relative Masses of the Elementary Molecules of Bodies", he essentially states, i.e. according to Partington's A Short History of Chemistry, that:

The smallest particles of gases are not necessarily simple atoms, but are made up of a certain number of these atoms united by attraction to form a single molecule.

In coordination with these concepts, in 1833 the French chemist Marc Antoine Auguste Gaudin presented a clear account of Avogadro's hypothesis, regarding atomic weights, by making use of "volume diagrams", which clearly show both semi-correct molecular geometries, such as a linear water molecule, and correct molecular formulas, such as H2O:

Marc Antoine Auguste Gaudin's volume diagrams of molecules in the gas phase (1833)

In 1917, an unknown American undergraduate chemical engineer named Linus Pauling was learning the Dalton hook-and-eye bonding method at the Oregon Agricultural College, which was the mainstream description of bonds between atoms at the time. Pauling, however, wasn't satisfied with this method and looked to the newly emerging field of quantum physics for a new method. In 1926, French physicist Jean Perrin received the Nobel Prize in physics for proving, conclusively, the existence of molecules. He did this by calculating Avogadro's number using three different methods, all involving liquid phase systems. First, he used a gamboge soap-like emulsion, second by doing experimental work on Brownian motion, and third by confirming Einstein's theory of particle rotation in the liquid phase.

In 1927, the physicists Fritz London and Walter Heitler applied the new quantum mechanics to the deal with the saturable, nondynamic forces of attraction and repulsion, i.e., exchange forces, of the hydrogen molecule. Their valence bond treatment of this problem, in their joint paper, was a landmark in that it brought chemistry under quantum mechanics. Their work was an influence on Pauling, who had just received his doctorate and visited Heitler and London in Zürich on a Guggenheim Fellowship.

Subsequently, in 1931, building on the work of Heitler and London and on theories found in Lewis' famous article, Pauling published his ground-breaking article "The Nature of the Chemical Bond" in which he used quantum mechanics to calculate properties and structures of molecules, such as angles between bonds and rotation about bonds. On these concepts, Pauling developed hybridization theory to account for bonds in molecules such as CH4, in which four sp³ hybridised orbitals are overlapped by hydrogen's 1s orbital, yielding four sigma (σ) bonds. The four bonds are of the same length and strength, which yields a molecular structure as shown below:

A schematic presentation of hybrid orbitals overlapping hydrogens' s orbitals

Molecular science

The science of molecules is called molecular chemistry or molecular physics, depending on whether the focus is on chemistry or physics. Molecular chemistry deals with the laws governing the interaction between molecules that results in the formation and breakage of chemical bonds, while molecular physics deals with the laws governing their structure and properties. In practice, however, this distinction is vague. In molecular sciences, a molecule consists of a stable system (bound state) composed of two or more atoms. Polyatomic ions may sometimes be usefully thought of as electrically charged molecules. The term unstable molecule is used for very reactive species, i.e., short-lived assemblies (resonances) of electrons and nuclei, such as radicals, molecular ions, Rydberg molecules, transition states, van der Waals complexes, or systems of colliding atoms as in Bose–Einstein condensate.

Prevalence

Molecules as components of matter are common. They also make up most of the oceans and atmosphere. Most organic substances are molecules. The substances of life are molecules, e.g. proteins, the amino acids of which they are composed, the nucleic acids (DNA and RNA), sugars, carbohydrates, fats, and vitamins. The nutrient minerals are generally ionic compounds, thus they are not molecules, e.g. iron sulfate.

However, the majority of familiar solid substances on Earth are made partly or completely of crystals or ionic compounds, which are not made of molecules. These include all of the minerals that make up the substance of the Earth, sand, clay, pebbles, rocks, boulders, bedrock, the molten interior, and the core of the Earth. All of these contain many chemical bonds, but are not made of identifiable molecules.

No typical molecule can be defined for salts nor for covalent crystals, although these are often composed of repeating unit cells that extend either in a plane, e.g. graphene; or three-dimensionally e.g. diamond, quartz, sodium chloride. The theme of repeated unit-cellular-structure also holds for most metals which are condensed phases with metallic bonding. Thus solid metals are not made of molecules. In glasses, which are solids that exist in a vitreous disordered state, the atoms are held together by chemical bonds with no presence of any definable molecule, nor any of the regularity of repeating unit-cellular-structure that characterizes salts, covalent crystals, and metals.

Bonding

Molecules are generally held together by covalent bonding. Several non-metallic elements exist only as molecules in the environment either in compounds or as homonuclear molecules, not as free atoms: for example, hydrogen.

While some people say a metallic crystal can be considered a single giant molecule held together by metallic bonding, others point out that metals behave very differently than molecules.

Covalent

A covalent bond forming H2 (right) where two hydrogen atoms share the two electrons
 

A covalent bond is a chemical bond that involves the sharing of electron pairs between atoms. These electron pairs are termed shared pairs or bonding pairs, and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is termed covalent bonding.

Ionic

Sodium and fluorine undergoing a redox reaction to form sodium fluoride. Sodium loses its outer electron to give it a stable electron configuration, and this electron enters the fluorine atom exothermically.

Ionic bonding is a type of chemical bond that involves the electrostatic attraction between oppositely charged ions, and is the primary interaction occurring in ionic compounds. The ions are atoms that have lost one or more electrons (termed cations) and atoms that have gained one or more electrons (termed anions). This transfer of electrons is termed electrovalence in contrast to covalence. In the simplest case, the cation is a metal atom and the anion is a nonmetal atom, but these ions can be of a more complicated nature, e.g. molecular ions like NH4+ or SO42−. At normal temperatures and pressures, ionic bonding mostly creates solids (or occasionally liquids) without separate identifiable molecules, but the vaporization/sublimation of such materials does produce separate molecules where electrons are still transferred fully enough for the bonds to be considered ionic rather than covalent.

Molecular size

Most molecules are far too small to be seen with the naked eye, although molecules of many polymers can reach macroscopic sizes, including biopolymers such as DNA. Molecules commonly used as building blocks for organic synthesis have a dimension of a few angstroms (Å) to several dozen Å, or around one billionth of a meter. Single molecules cannot usually be observed by light (as noted above), but small molecules and even the outlines of individual atoms may be traced in some circumstances by use of an atomic force microscope. Some of the largest molecules are macromolecules or supermolecules.

The smallest molecule is the diatomic hydrogen (H2), with a bond length of 0.74 Å.

Effective molecular radius is the size a molecule displays in solution. The table of permselectivity for different substances contains examples.

Molecular formulas

Chemical formula types

The chemical formula for a molecule uses one line of chemical element symbols, numbers, and sometimes also other symbols, such as parentheses, dashes, brackets, and plus (+) and minus (−) signs. These are limited to one typographic line of symbols, which may include subscripts and superscripts.

A compound's empirical formula is a very simple type of chemical formula. It is the simplest integer ratio of the chemical elements that constitute it. For example, water is always composed of a 2:1 ratio of hydrogen to oxygen atoms, and ethanol (ethyl alcohol) is always composed of carbon, hydrogen, and oxygen in a 2:6:1 ratio. However, this does not determine the kind of molecule uniquely – dimethyl ether has the same ratios as ethanol, for instance. Molecules with the same atoms in different arrangements are called isomers. Also carbohydrates, for example, have the same ratio (carbon:hydrogen:oxygen= 1:2:1) (and thus the same empirical formula) but different total numbers of atoms in the molecule.

The molecular formula reflects the exact number of atoms that compose the molecule and so characterizes different molecules. However different isomers can have the same atomic composition while being different molecules.

The empirical formula is often the same as the molecular formula but not always. For example, the molecule acetylene has molecular formula C2H2, but the simplest integer ratio of elements is CH.

The molecular mass can be calculated from the chemical formula and is expressed in conventional atomic mass units equal to 1/12 of the mass of a neutral carbon-12 (12C isotope) atom. For network solids, the term formula unit is used in stoichiometric calculations.

Structural formula

3D (left and center) and 2D (right) representations of the terpenoid molecule atisane
 

For molecules with a complicated 3-dimensional structure, especially involving atoms bonded to four different substituents, a simple molecular formula or even semi-structural chemical formula may not be enough to completely specify the molecule. In this case, a graphical type of formula called a structural formula may be needed. Structural formulas may in turn be represented with a one-dimensional chemical name, but such chemical nomenclature requires many words and terms which are not part of chemical formulas.

Molecular geometry

Structure and STM image of a "cyanostar" dendrimer molecule.

Molecules have fixed equilibrium geometries—bond lengths and angles— about which they continuously oscillate through vibrational and rotational motions. A pure substance is composed of molecules with the same average geometrical structure. The chemical formula and the structure of a molecule are the two important factors that determine its properties, particularly its reactivity. Isomers share a chemical formula but normally have very different properties because of their different structures. Stereoisomers, a particular type of isomer, may have very similar physico-chemical properties and at the same time different biochemical activities.

Molecular spectroscopy

Hydrogen can be removed from individual H2TPP molecules by applying excess voltage to the tip of a scanning tunneling microscope (STM, a); this removal alters the current-voltage (I-V) curves of TPP molecules, measured using the same STM tip, from diode like (red curve in b) to resistor like (green curve). Image (c) shows a row of TPP, H2TPP and TPP molecules. While scanning image (d), excess voltage was applied to H2TPP at the black dot, which instantly removed hydrogen, as shown in the bottom part of (d) and in the rescan image (e). Such manipulations can be used in single-molecule electronics.

Molecular spectroscopy deals with the response (spectrum) of molecules interacting with probing signals of known energy (or frequency, according to Planck's formula). Molecules have quantized energy levels that can be analyzed by detecting the molecule's energy exchange through absorbance or emission. Spectroscopy does not generally refer to diffraction studies where particles such as neutrons, electrons, or high energy X-rays interact with a regular arrangement of molecules (as in a crystal).

Microwave spectroscopy commonly measures changes in the rotation of molecules, and can be used to identify molecules in outer space. Infrared spectroscopy measures the vibration of molecules, including stretching, bending or twisting motions. It is commonly used to identify the kinds of bonds or functional groups in molecules. Changes in the arrangements of electrons yield absorption or emission lines in ultraviolet, visible or near infrared light, and result in colour. Nuclear resonance spectroscopy measures the environment of particular nuclei in the molecule, and can be used to characterise the numbers of atoms in different positions in a molecule.

Theoretical aspects

The study of molecules by molecular physics and theoretical chemistry is largely based on quantum mechanics and is essential for the understanding of the chemical bond. The simplest of molecules is the hydrogen molecule-ion, H2+, and the simplest of all the chemical bonds is the one-electron bond. H2+ is composed of two positively charged protons and one negatively charged electron, which means that the Schrödinger equation for the system can be solved more easily due to the lack of electron–electron repulsion. With the development of fast digital computers, approximate solutions for more complicated molecules became possible and are one of the main aspects of computational chemistry.

When trying to define rigorously whether an arrangement of atoms is sufficiently stable to be considered a molecule, IUPAC suggests that it "must correspond to a depression on the potential energy surface that is deep enough to confine at least one vibrational state". This definition does not depend on the nature of the interaction between the atoms, but only on the strength of the interaction. In fact, it includes weakly bound species that would not traditionally be considered molecules, such as the helium dimer, He2, which has one vibrational bound state and is so loosely bound that it is only likely to be observed at very low temperatures.

Whether or not an arrangement of atoms is sufficiently stable to be considered a molecule is inherently an operational definition. Philosophically, therefore, a molecule is not a fundamental entity (in contrast, for instance, to an elementary particle); rather, the concept of a molecule is the chemist's way of making a useful statement about the strengths of atomic-scale interactions in the world that we observe.

Memory and trauma

From Wikipedia, the free encyclopedia https://en.wikipedia.org/wiki/Memory_and_trauma ...